Supplementary Information for Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae

Max E. Schön, Vasily V. Zlatogursky, Rohan P. Singh, Camille Poirier, Susanne Wilken, Varsha Mathur, Jürgen F. H. Strassert, Jarone Pinhassi, Alexandra Z. Worden, Patrick J. Keeling, Thijs J. G. Ettema, Jeremy G. Wideman, Fabien Burki*

List of Figures

1 Maximum Likelihood tree of the 18S rRNA gene...... 3

2 Combined relative abundance of all Picozoa OTUs identified in the Tara Oceans metabarcoding data...... 4

3 Maximum likelihood tree of 794 eukaryotic species...... 5

4 Support for several groupings as estimated in different trees with increasing number of fast- evolving sites removed...... 6

5 Maximum likelihood tree of 67 eukaryotic species showing the position of Picozoa...... 6

6 Multi-species coalescent species tree reconstructed with ASTRAL-III...... 7

7 Maximum likelihood tree of 67 eukaryotic species showing the position of Picozoa...... 8

8 Maximum likelihood tree of 67 eukaryotic species showing the position of Picozoa...... 9

9 Complete and near complete mitochondrial genomes assembled from diverse picozoan SAGs. . 10

10 Number of inferred lateral gene transfers (LGT) across a selection of 33 species...... 11

11 Maximum Likelihood tree of the 18S rRNA gene from the individual SAG assemblies and an extended number of reference sequences from Picozoa and other major eukaryotic groups from the PR2 database...... 12

12 Heatmap showing pairwise ANI for 43 initial picozoan SAGs as estimated with FastANI...... 13

13 Boxplots of different BUSCO categories (Missing, Complete, Fragmented and Duplicated) for all selected SAGs/Co-SAGs...... 13

14 Contamination estimate for each of the 17 final SAGs/Co-SAGs...... 14

15 Maximum likelihood tree of eukaryotic species showing the position of Picozoa...... 15

16 Bayesian phylogenetic tree made using PhyloBayes...... 16

17 Bayesian phylogenetic tree made using PhyloBayes...... 17

List of Tables

1 Assembly/genome characteristics SAGs and CO-SAGs ...... 18

1 2 Additional genomes added to the Phylogenomic dataset ...... 18 3 Phylogenomic dataset taxon selection and taxon merging ...... 18 4 Results from the AU and other topology tests performed with IQ-TREE ...... 18 5 The Picozoan MS584-11 mitochondrial genome was used as a BLAST query into the 43 picozoan SAGs...... 18 6 Commonly retained plastid pathways and proteins ...... 18 7 EGT clustering dataset taxon selection ...... 18 8 Phylogenomic dataset taxon selection and taxon merging ...... 18 9 EGT and LGT results for 33 selected species/groups ...... 18 1 untrimmed EEF2 alignment ...... 18

2 3 0 SAG17_NODE_209_length_6604_cov_12.631822_939-2744 2 7 'BP1' 3 0 SAG41_NODE_729_length_1138_cov_22.611165_1-553 9 SAG09_NODE_597_length_2008_cov_1.544264_102-784 SAG43_NODE_6386_length_1046_cov_569.933474_20-1046 3 2 SAG16_NODE_467_length_2239_cov_20.097664_535-2239 6 5 JX988764.1.1138_U_clone_PICOBI01F-L52R_10 4 9 1 2 KJ763213.1.1806_U_clone_SGUH612 COSAG02 SAG41_NODE_563_length_1533_cov_4.731520_304-1533 2 0 SAG35_NODE_69_length_11959_cov_32.509528_8945-10750 2 79 SAG21_NODE_816_length_2079_cov_2.398990_290-2079 6 5 SAG32_NODE_791_length_6633_cov_1359.747626_737-2542 SAG18_NODE_1586_length_1284_cov_1.328270_750-1215 8 SAG34_NODE_220_length_626_cov_0.867173_100-625 6 7 EU368003.1.1109_U_clone_FS01AA11_01Aug05_5m 9 5 EU368004.1.1126_U_clone_FS01AA94_01Aug05_5m 24 3 5 EU368020.1.1039_U_clone_FS04GA95_01Aug05_5m 100 DQ222876.1.1799_U_clone_RA000907.33 4 2 JF791041.1.1777_U_clone_7532 SAG18_NODE_3756_length_534_cov_0.671264_2-533 8 9 JX988758.1.1807_U_Picomonas_judraskeda 5 2 8 0 SAG01_NODE_1281_length_3345_cov_9.888478_301-2106 4 1 HQ867389.1.887_U_clone_SHAC701 COSAG03 SAG40_NODE_1486_length_1870_cov_3.223602_876-1870 4 5 SAG02_NODE_164_length_1182_cov_0.938135_1-1175 100 HQ869261.1.1000_U_clone_SHBA597 4 5 4 8 HQ869362.1.935_U_clone_SHBA707 14 73 SAG09_NODE_2410_length_432_cov_0.936937_1-430 KC488338.1.1714_U_clone_HL2SCM10.71 3 8 SAG36_NODE_269_length_5276_cov_1081.533127_3-1607 SAG26_NODE_716_length_5622_cov_237.617237_668-2473 6 5 SAG39_NODE_1105_length_5866_cov_172.926131_882-2687 COSAG06 5 8 SAG30_NODE_204_length_11251_cov_42.867737_1433-3238 7 9 SAG27_NODE_219_length_12917_cov_16.477298_7670-9475 5 3 JN934893.1_Picobiliphyte_SAG_sp._MS609-66 7 8 JN934890.1_Picobiliphyte_SAG_MS584-5 KJ762479.1.1805_U_clone_SGYH1057 JQ226352.1.1606_U_clone_SHAA389 3 6 4 3 KF031848.1.1765_U_clone_CC02A175.091 8 0 KJ173845.1.986_U_clone_DH117-1000m-C02 7 9100 SAG23_NODE_141_length_11148_cov_11.089963_3919-5724 COSAG04 SAG19_NODE_794_length_9268_cov_1638.280401_2687-4492 KJ173847.1.992_U_clone_DH117-1000m-C10 6 7 HQ868776.1.919_U_clone_SHAX1019 100 7 7 HQ868797.1.923_U_clone_SHAX1043 7 4 HQ868690.1.947_U_clone_SHAX927 4 0 KJ759275.1.1806_U_clone_SGYO1039 7 1 SAG08_NODE_2796_length_1578_cov_105.795132_5-1572 3 1 SAG42_NODE_33_length_26034_cov_34.003856_573-2378 SAG29_NODE_208_length_10399_cov_14.269126_3742-5547 7 0 SAG13_NODE_154_length_12455_cov_60.081013_5953-7758 COSAG01 8 4 SAG04_NODE_206_length_16512_cov_7.695729_11513-13318 6 1 9 9 SAG24_NODE_30_length_15199_cov_8.991656_4494-6299 9 0 SAG20_NODE_95_length_11004_cov_58.023107_5150-6955 SAG12_NODE_286_length_10619_cov_339.861977_9641-10619 KJ762972.1.1807_U_clone_SGUH1326 5 3 HQ869099.1.906_U_clone_SHAX616 4 5 6 3 100 HQ869574.1.909_U_clone_SHBF544 4 1 HQ869605.1.957_U_clone_SHBF578 6 1 HQ869692.1.905_U_clone_SHBF671 9 9 KC488345.1.1706_U_clone_HL5aSF04.93 JQ222911.1.1637_U_clone_SHAU435 6 6 HM561168.1.984_U_clone_CFL146DB13 3 8 SAG38_NODE_1157_length_2077_cov_56.130515_304-2077 7 2 3 8 SAG14_NODE_6_length_54255_cov_1799.083795_52455-54255 8 1 SAG06_NODE_69_length_968_cov_0.676640_12-968 SAG06_NODE_305_length_411_cov_0.810897_3-411 6 6 9 8 EU368037.1.1764_U_clone_EN351CTD039_30mN9 COSAG05 8 3 9 9 JN934891.1_Picobiliphyte_SAG_sp._MS584-11 'BP3' SAG15_NODE_683_length_4737_cov_2550.787193_738-2541 7 1 KJ173846.1.991_U_clone_DH117-1000m-C07 KJ173838.1.862_U_clone_DH113-5m-D02 100 DQ222875.1.1801_U_clone_OR000415.159 6 7 100 JN934892.1_Picobiliphyte_SAG_sp._MS584-22 HQ867491.1.910_U_clone_SHAH476 9 9 HQ867421.1.875_U_clone_SHAC745 7 1 8 1 KF130491.1.1763_U_clone_ST8360.104 SAG22_NODE_175_length_16235_cov_67.112729_1670-3473 8 5 9 8 DQ222874.1.1786_U_clone_HE001005.148 JX988767.1.1135_U_clone_PICOBI02F-L52R_He 9 9 EU368021.1.1096_U_clone_FS04GA46_01Aug05_5m 100 9 3 AY426835.1.1803_U_clone_BL000921.8 SAG31_NODE_544_length_14245_cov_68.376644_6887-8690 'BP2' 8 0 HQ869075.1.930_U_clone_SHAX587 8 2 100 100 JX840937.1.1271_U_clone_ARK_21 KJ173843.1.991_U_clone_DH116-100m-C03 'Deep branching Picozoa 1' KJ173850.1.854_U_clone_DH117-1000m-D03 7 4 100 KJ763562.1.1796_U_clone_SGYP1354 SAG11_NODE_229_length_11945_cov_77.865187_857-2654 8 9 6 0 DQ060528.1.800_U_clone_NOR50.25 100 DQ060527.1.1237_U_clone_NOR50.52 9 2 KC488340.1.1697_U_clone_HL5aSCM04.10 9 8 HM561172.1.953_U_clone_CFL119DB12 8 8 6 6 KJ762470.1.1800_U_clone_SGYH1041 'Deep branching Picozoa 2' 100 KC488342.1.1710_U_clone_HL5aSCM04.38 HQ868882.1.878_U_clone_SHAX1135 KC488336.1.1682_U_clone_BBL1SF10.02 9 9 HQ867420.1.880_U_clone_SHAC744 5 7 8 6 HQ867337.1.876_U_clone_SHAC623 5 0 HQ867471.1.868_U_clone_SHAC426 4 6 8 9 AY343928.1.1812_U_clone_He000803-72 2 2 KJ759623.1.1791_U_clone_SGYO702 KC488339.1.1675_U_clone_HL2SF10.08 5 6 GU824414.1.1057_U_clone_AA5F13RM2D10 7 5 100 HQ867331.1.869_U_clone_SHAC614 4 7 HQ867442.1.871_U_clone_SHAC390 3 5 DQ060524.1.1778_U_clone_NW414.27 SAG28_NODE_1308_length_928_cov_36.342746_1-913 7 1 HQ866220.1.881_U_clone_SGSP644 8 1 7 3 HQ869572.1.881_U_clone_SHBF542 KC488334.1.1687_U_clone_BBL1SCM04.08 9 9 100 EU561759.1.879_U_clone_IND31.88 KJ759641.1.1788_U_clone_SGYO733 HQ867427.1.876_U_clone_SHAC752 8 9 FN689854.1.826_U_clone_He040503_11A HQ864893.1.880_U_clone_SGPX462 100 U53126.1.1756_U_strain_CCMP_325_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Hanusia_Hanusia_phi 6 9 4 3 X57162.1.1773_U__Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Guillardia_Guillardia_theta 7 2 L28811.1.1763_U_strain_CCAP_977_2a_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Cryptomonas_Cryptomonas_paramecium 9 2 HM126532.1.1732_U_strain_K-1487_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Rhodomonas_Rhodomonas_salina 8 3 AJ007285.1.1761_U_strain_CCMP_704_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Proteomonas_Proteomonas_sulcata 9 7 AM901350.1.1670_U_strain_CCMP_441_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Hemiselmis_Hemiselmis_andersenii JF790986.1.1777_U_clone_1126_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Geminigera_Geminigera_cryophila AF508277.1.1721_U_strain_CCMP1869_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Goniomonadales_Goniomonadales_X_Goniomonas_Goniomonas_pacifica 100 HQ191366.1.1830_U_clone_PA2009C5_Eukaryota_Hacrobia_Katablepharidophyta_Katablepharidaceae_Katablepharidales_Katablepharidales_X_Katablepharidales_XX_Katablepharidales_XX_sp. 9 9 2 7 GU068005.1.1774_U_clone_ESS241006.012_Eukaryota_Hacrobia_Katablepharidophyta_Katablepharidaceae_Katablepharidales_Katablepharidales_X_Katablepharidales_XX_Katablepharidales_XX_sp. 8 6 6 4 KJ925375.1.1690_U_clone_275D08_Eukaryota_Hacrobia_Katablepharidophyta_Katablepharidaceae_Katablepharidales_Katablepharidales_X_Katablepharidales_XX_Katablepharidales_XX_sp. 8 7 KJ925380.1.1702_U_clone_275E02._Eukaryota_Hacrobia_Katablepharidophyta_Katablepharidaceae_Katablepharidales_Katablepharidales_X_Katablepharidales_XX_Katablepharidales_XX_sp. 8 6 KJ762967.1.1799_U_clone_SGUH1318_Eukaryota_Hacrobia_Katablepharidophyta_Katablepharidaceae_Katablepharidales_Katablepharidales_X_Leucocryptos_Leucocryptos_marina JP445963.602.2392_U__Eukaryota_Hacrobia_Katablepharidophyta_Katablepharidaceae_Katablepharidales_Katablepharidales_X_Roombia_Roombia_truncata GU823724.1.1189_U_clone_AA5F15RM2F06_Eukaryota_Hacrobia_Katablepharidophyta_Katablepharidaceae_Katablepharidales_Katablepharidales_X_Katablepharidales_XX_Katablepharidales_XX_sp.

0.06 Supplementary Figure 1: Maximum Likelihood tree of the 18S rRNA gene. Sequences from the individual SAG assemblies and a number of reference sequences from Picozoa, cryptophyes katablepharids from the PR2 database. The tree was reconstructed under the model GTR+G.

3 0.1% 1% 10% 30% SAG sampling

Supplementary Figure 2: Combined relative abundance of all Picozoa OTUs identified in the Tara Oceans metabarcoding data. Abundances are given on a corresponding map of sampling locations. Size of the circles corresponds to relative abundance. Triangles mark the location of single-cell sampling from this study.

4 18 24 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_marinoi_skelA 30 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_marinoi_SM1012Den-03 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_marinoi_SM1012Hels-07 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_costatum_1716 100100Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_marinoi_FE60 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_marinoi_FE7 53 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_marinoi_UNC1201 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_dohrnii_SkelB 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_japonicum_CCMP2506 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_grethae_CCMP1804 100Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Skeletonemataceae_Skeletonema_menzellii_CCMP793 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_rotula_GSO102 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_rotula_CCMP3096 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_gravida_GMp14c1 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_punctigera_Tpunct2005C2 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_antarctica_CCMP982 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_minuscula_CCMP1093 100100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_sp_NH16 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Detonula_confervacea_CCMP353 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_oceanica_ThaOc_1.0 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_pseudonana_N/A Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_sp_FW 99 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Stephanodiscaceae_Cyclotella_meneghiniana_CCMP338 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_weissflogii_CCMP1336 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_weissflogii_CCMP1010 100 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Lithodesmiales_Lithodesmiaceae_Ditylum_brightwellii_GSO105 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Lithodesmiales_Lithodesmiaceae_Ditylum_brightwellii_GSO103 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Lithodesmiales_Lithodesmiaceae_Helicotheca_tamesis_CCMP826100 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Chaetocerotales_Chaetocerotaceae_Chaetoceros_brevis_CCMP164 85 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Chaetocerotales_Chaetocerotaceae_Chaetoceros_debilis_MM31A-1 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Chaetocerotales_Chaetocerotaceae_Chaetoceros_curvisetus_js001 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Chaetocerotales_Chaetocerotaceae_Chaetoceros_sp_UNC1202 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Chaetocerotales_Chaetocerotaceae_Chaetoceros_sp_GSL56 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Chaetocerotales_Chaetocerotaceae_Chaetoceros_neogracile_RCC1993 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Chaetocerotales_Chaetocerotaceae_Chaetoceros_neogracile_CCMP1317 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Chaetocerotales_Chaetocerotaceae_Chaetoceros_affinis_CCMP159 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Chaetocerotales_Chaetocerotaceae_Chaetoceros_dichaeta_CCMP1751 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_N/A_Rhizosoleniaceae_Dactyliosolen_fragilissimus_js002 100 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Hemiaulales_Hemiaulaceae_Eucampia_antarctica_CCMP1452 99 100 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Cymatosirales_Cymatosiraceae_Minutocellus_polymorphus_CCMP3303 100 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Cymatosirales_Cymatosiraceae_Minutocellus_polymorphus_NH13 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Cymatosirales_Cymatosiraceae_Minutocellus_polymorphus_RCC2270 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Cymatosirales_Cymatosiraceae_Extubocellulus_spinifer_CCMP396 100 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Triceratiales_Triceratiaceae_Triceratium_dubium_CCMP147 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Eupodiscales_Eupodiscaceae_Odontella_aurita_isolate1302-5 Stramenopila-Ochrophyta_Bacillariophyta_Mediophyceae_Eupodiscales_Eupodiscaceae_Odontella_sinensis_Grunow1884100 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Pseudo-nitzschia_delicatissima_UNC1205 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Pseudo-nitzschia_delicatissima_B596 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Pseudo-nitzschia_arenysensis_B593 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Pseudo-nitzschia_heimii_UNC1101 100 100Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Pseudo-nitzschia_fraudulenta_WWA7 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Pseudo-nitzschia_pungens_cf.pungens 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Pseudo-nitzschia_pungens_cf.cingulata Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Pseudonitzschia_multiseries_N/A 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Pseudo-nitzschia_australis_1024910AB 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Fragilariopsis_cylindrus_N/A Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Tryblionella_compressa_CCMP561 100 97 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Nitzschia_sp_RCC80 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Peridiniaceae_Kryptoperidinium_foliaceum-endo_CCAP1116_3 100 98 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Peridiniaceae_Durinskia_baltica-endo_CSIROCS-38 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Peridiniaceae_Kryptoperidinium_foliaceum-endo_CCMP1326 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Bacillariales_Bacillariaceae_Cylindrotheca_closterium_KMMCC_B-181 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Naviculales_Stauroneidaceae_Stauroneis_constricta_CCMP1120 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Naviculales_Naviculaceae_Craspedostauros_australis_CCMP3328 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Naviculales_Amphipleuraceae_Amphiprora_paludosa_CCMP125 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Naviculales_Amphipleuraceae_Amphiprora_sp_CCMP467 100 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_N/A_Entomoneidaceae_Entomoneis_sp_CCMP2396 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Thalassiophysales_Catenulaceae_Amphora_coffeiformis_CCMP127 Stramenopila-Ochrophyta_Bacillariophyta_Bacillariophyceae_Naviculales_Phaeodactylaceae_Phaeodactylum_tricornutum_N/A 100 100 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Thalassionemales_Thalassionemataceae_Thalassionema_nitzschioides_L26-B 100 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Thalassionemales_Thalassionemataceae_Thalassionema_frauenfeldii_CCMP1798 100 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Thalassionemales_Thalassionemataceae_Thalassiothrix_antarctica_L6-D1 100 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Fragilariales_Fragilariaceae_Synedropsis_recta_CCMP1620 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_N/A_Licmophoraceae_Licmophora_paradoxa_CCMP2313 100 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Cyclophorales_Cyclophoraceae_Astrosyne_radiata_13vi08-1A 83 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Cyclophorales_Cyclophoraceae_Cyclophora_tenuis_ECT3854 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Striatellales_Grammatophoraceae_Grammatophora_oceanica_CCMP410 100 100 100 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Fragilariales_Fragilariaceae_Staurosira_complex_CCMP2646 100 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Fragilariales_Fragilariaceae_Asterionellopsis_glacialis_CCMP134 100 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Fragilariales_Fragilariaceae_Asterionellopsis_glacialis_N/A Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Fragilariales_Fragilariaceae_Asterionellopsis_glacialis_CCMP1581 Stramenopila-Ochrophyta_Bacillariophyta_Fragilariophyceae_Striatellales_Striatellaceae_Striatella_unipunctata_CCMP2910 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Chaetocerotales_Attheyaceae_Attheya_septentrionalis_CCMP2084 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_N/A_Rhizosoleniaceae_Rhizosolenia_setigera_CCMP1694 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Coscinodiscales_Coscinodiscaceae_Coscinodiscus_wailesii_CCMP2513 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_N/A_Rhizosoleniaceae_Proboscia_alata_PI-D3 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_N/A_Rhizosoleniaceae_Proboscia_inermis_CCAP1064_1 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_N/A_Aulacoseiraceae_Aulacoseira_subarctica_CCAP1002_5 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Melosirales_Stephanopyxidaceae_Stephanopyxis_turris_CCMP815 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_N/A_Leptocylindraceae_Leptocylindrus_danicus_CCMP1856 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_N/A_Leptocylindraceae_Leptocylindrus_danicus_B650 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_N/A_Leptocylindraceae_Leptocylindrus_danicus_B651 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Corethrales_Corethraceae_Corethron_hystrix_308 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Corethrales_Corethraceae_Corethron_pennatum_L29A3 97 100 Stramenopila-Ochrophyta_Bolidophyceae_N/A_N/A_N/A_Bolidomonas_sp_RCC2347 100 Stramenopila-Ochrophyta_Bolidophyceae_N/A_N/A_N/A_Bolidomonas_pacifica_RCC208 Stramenopila-Ochrophyta_Bolidophyceae_N/A_N/A_N/A_Bolidomonas_sp_RCC1657 Stramenopila-Ochrophyta_Bolidophyceae_N/A_N/A_N/A_Bolidomonas_pacifica_CCMP1866 100 Stramenopila-Ochrophyta_Pinguiophyceae_N/A_Pinguiochrysidales_Pinguiochrysidaceae_Phaeomonas_parva_CCMP2877 100Stramenopila-Ochrophyta_Pinguiophyceae_N/A_Pinguiochrysidales_Pinguiochrysidaceae_Pinguiococcus_pyrenoidosus_CCMP2078 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Pelagomonadales_N/A_Pelagomonas_calceolata_CCMP1756 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Pelagomonadales_N/A_Pelagomonas_calceolata_RCC969 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Pelagomonadales_N/A_Pelagococcus_subviridis_CCMP1429 97 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Pelagomonadales_N/A_N/A_N/A_RCC1024 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Pelagomonadales_N/A_Aureococcus_anophagefferens_N/A Stramenopila-Ochrophyta_N/A_Pelagophyceae_N/A_N/A_N/A_N/A_CCMP2097 100 100 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Sarcinochrysidales_Sarcinochrysidaceae_N/A_N/A_CCMP2135 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Sarcinochrysidales_Sarcinochrysidaceae_Chrysoreinhardia_sp_CCMP3193 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Sarcinochrysidales_Sarcinochrysidaceae_Aureoumbra_lagunensis_CCMP1510 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Sarcinochrysidales_Sarcinochrysidaceae_Chrysoreinhardia_sp_CCMP2950 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Sarcinochrysidales_Sarcinochrysidaceae_Sarcinochrysis_sp_CCMP770 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Sarcinochrysidales_Sarcinochrysidaceae_Chrysocystis_fragilis_CCMP3189 100 93 100 Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Florenciellales_N/A_Florenciella_sp_RCC1587 100 Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Florenciellales_N/A_Florenciella_parvula_RCC1693 100 Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Florenciellales_N/A_Florenciella_parvula_CCMP2471 100 Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Florenciellales_N/A_Florenciella_sp_RCC1007 82 Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Florenciellales_N/A_Pseudochattonella_farcimen_N/A Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Dictyochales_N/A_Dictyocha_speculum_CCMP1381 100 100 Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Pedinellales_N/A_Pteridomonas_sp_PT 100 Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Pedinellales_N/A_Pteridomonas_danica_PT 100 100 Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Pedinellales_N/A_N/A_N/A_CCMP2098 Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Pedinellales_N/A_Pseudopedinella_elastica_CCMP716 100 Stramenopila-Ochrophyta_N/A_Dictyochophyceae_Rhizochromulinales_N/A_Rhizochromulina_marina_CCMP1243 100 Stramenopila-Ochrophyta_Xanthophyceae_N/A_Tribonematales_Tribonemataceae_Tribonema_aequale_N/A 100 Stramenopila-Ochrophyta_Xanthophyceae_N/A_Vaucheriales_Vaucheriaceae_Vaucheria_litorea_CCMP2940 100 Stramenopila-Ochrophyta_Phaeophyceae_N/A_Laminariales_Laminariaceae_Laminaria_sp_N/A 100 Stramenopila-Ochrophyta_Phaeophyceae_N/A_Ectocarpales_Ectocarpaceae_Ectocarpus_siliculosus_N/A 100 Stramenopila-Ochrophyta_N/A_Raphidophyceae_Chattonellales_Chattonellaceae_Chattonella_subsalsa_CCMP2191 84 Stramenopila-Ochrophyta_N/A_Raphidophyceae_Chattonellales_Chattonellaceae_Heterosigma_akashiwo_CCMP2393 100 Stramenopila-Ochrophyta_N/A_Raphidophyceae_Chattonellales_Chattonellaceae_Fibrocapsa_japonica_CCMP1661 88 Stramenopila-Ochrophyta_Eustigmatophyceae_N/A_Eustigmatales_Monodopsidaceae_Nannochloropsis_granulata_N/A 100 Stramenopila-Ochrophyta_Eustigmatophyceae_N/A_Eustigmatales_Monodopsidaceae_Nannochloropsis_gaditana_NagaB31_1.0 99 Stramenopila-Ochrophyta_Eustigmatophyceae_N/A_Eustigmatales_Monodopsidaceae_Nannochloropsis_gaditana_N/A Stramenopila-Ochrophyta_Eustigmatophyceae_N/A_Eustigmatales_Monodopsidaceae_Nannochloropsis_gaditana_ASM24072v1100 100 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Chromulinaceae_N/A_N/A_CCMP2298 100 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Chromulinaceae_Ochromonas_sp_CCMP1393 100 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Chromulinaceae_Spumella_elongata_CCAP955_1 100 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Dinobryaceae_Dinobryon_sp_UTEXLB2267 100 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Chromulinaceae_Ochromonas_sp_BG-1 72 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Chromulinaceae_Chromulina_nebulosa_UTEXLB2642 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Chromulinaceae_Ochromonas_sp_CCMP1899 100 100 Stramenopila-Ochrophyta_N/A_Synurophyceae_Synurales_Mallomonadaceae_Mallomonas_sp_CCMP3275 100 100 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Paraphysomonadaceae_Paraphysomonas_vestita_GFlagA Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Paraphysomonadaceae_Paraphysomonas_bandaiensis_js007 100 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Paraphysomonadaceae_Paraphysomonas_imperforata_PA2 100 Stramenopila-Ochrophyta_N/A_Synchromophyceae_N/A_N/A_Synchroma_pusillum_CCMP3072 100 Stramenopila-Oomycota_N/A_Oomycetes_Peronosporales_Peronosporaceae_Plasmopara_halstedii_Plasmopara_halstedii_genome Stramenopila-Oomycota_N/A_Oomycetes_Peronosporales_N/A_Phytophthora_infestans_ASM14294v1 93 Stramenopila-Oomycota_N/A_Oomycetes_Peronosporales_N/A_Phytophthora_capsici_N/A 100100 Stramenopila-Oomycota_N/A_Oomycetes_Peronosporales_N/A_Phytophthora_sojae_N/A Stramenopila-Oomycota_N/A_Oomycetes_Peronosporales_N/A_Phytophthora_sojae_P_sojae_V3_0 100 100 Stramenopila-Oomycota_N/A_Oomycetes_Peronosporales_N/A_Phytophthora_ramorum_N/A 100 Stramenopila-Oomycota_N/A_Oomycetes_Peronosporales_N/A_Phytophthora_ramorum_ASM14973v1 100 Stramenopila-Oomycota_N/A_Oomycetes_Peronosporales_Peronosporaceae_Hyaloperonospora_arabidopsidis_HyaAraEmoy2_2.0 100 Stramenopila-Oomycota_N/A_Oomycetes_Peronosporales_N/A_Phytopythium_vexans_GCA_000387545.2 100 100 Stramenopila-Oomycota_N/A_Oomycetes_Pythiales_Pythiaceae_Pythium_arrhenomanes_N/A 72 Stramenopila-Oomycota_N/A_Oomycetes_Pythiales_Pythiaceae_Pythium_arrhenomanes_GCA_000387505.2 100 Stramenopila-Oomycota_N/A_Oomycetes_Pythiales_Pythiaceae_Pythium_oligandrum_N/A 100 Stramenopila-Oomycota_N/A_Oomycetes_Albuginales_Albuginaceae_Albugo_laibachii_ENA1 Stramenopila-Oomycota_N/A_Oomycetes_Albuginales_Albuginaceae_Albugo_candida_ASM107853v1 100 Stramenopila-Oomycota_N/A_Oomycetes_Saprolegniales_Saprolegniaceae_Aphanomyces_invadans_Apha_inva_NJM9701_V1 100 Stramenopila-Oomycota_N/A_Oomycetes_Saprolegniales_Saprolegniaceae_Aphanomyces_astaci_Apha_asta_APO3_V1 100 Stramenopila-Oomycota_N/A_Oomycetes_Saprolegniales_Saprolegniaceae_Saprolegnia_diclina_Sap_diclina_VS20_V1 100 Stramenopila-Oomycota_N/A_Oomycetes_Saprolegniales_Saprolegniaceae_Saprolegnia_parasitica_N/A 59 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Schizochytrium_aggregatum_N/A Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Thraustochytrium_sp_LLF1b 100 100 100 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Aurantiochytrium_limacinum_N/A 100 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_N/A_N/A_NY0313808BC1 100 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_N/A_N/A_NY070348D 100 100 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Aplanochytrium_sp_PBS07 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Aplanochytrium_kerguelense_N/A Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Aplanochytrium_stocchinoi_GSBS06 100 Stramenopila-Sagenista_MAST_N/A_N/A_N/A_N/A_N/A_MAST4 100 Stramenopila-Opalozoa_N/A_N/A_N/A_N/A_Blastocystis_sp_subtype_4 100 Stramenopila-Opalozoa_N/A_N/A_N/A_N/A_Blastocystis_hominis_N/A 100 Stramenopila-Opalozoa_N/A_N/A_N/A_N/A_Incisomonas_marina_CCAP997_1 Stramenopila-Opalozoa_Bicosoecida_N/A_Bicosoecida_Cafeteriaceae_Cafeteria_sp_CaronLabIsolate 100 Stramenopila-Opalozoa_Bicosoecida_N/A_Bicosoecida_Cafeteriaceae_Cafeteria_roenbergensis_E4-10 Stramenopila-Opalozoa_Bicosoecida_N/A_Bicosoecida_N/A_Bicosoecida_sp_ms1100 100 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_C1 100 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_C15 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_kawagutii_CCMP2468 100 100 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_minutum_N/A 100 100 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_N/A Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_CCMP2430 100 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_Mp 95 Alveolata_Dinophyta_Dinophyceae_Suessiales_Suessiaceae_Pelagodinium_beii_RCC1491 100 Alveolata_Dinophyta_Dinophyceae_Suessiales_Suessiaceae_Polarella_glacialis_CCMP1383 95 Alveolata_Dinophyta_Dinophyceae_Prorocentrales_Prorocentraceae_Prorocentrum_minimum_CCMP2233 Alveolata_Dinophyta_Dinophyceae_Prorocentrales_Prorocentraceae_Prorocentrum_minimum_CCMP1329 100Alveolata_Dinophyta_Dinophyceae_Prorocentrales_Prorocentraceae_Prorocentrum_lima_CCMP684 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Thoracosphaeraceae_Scrippsiella_hangoei_SHTV-5 90 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Thoracosphaeraceae_N/A_N/A_SHHI-4 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Peridiniaceae_Peridinium_aciculiferum_PAER-2 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Crypthecodiniaceae_Crypthecodinium_cohnii_Seligo 100 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Thoracosphaeraceae_Scrippsiella_trochoidea_CCMP3099 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Peridiniaceae_Kryptoperidinium_foliaceum_CCMP1326 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Peridiniaceae_Kryptoperidinium_foliaceum_CCAP1116_3 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Peridiniaceae_Durinskia_baltica_CSIROCS-38 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Endodiniaceae_Brandtodinium_nutricula_RCC3387 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Heterocapsaceae_Heterocapsa_arctica_CCMP445 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Heterocapsaceae_Heterocapsa_rotundata_SCCAPK-0483 100Alveolata_Dinophyta_Dinophyceae_Peridiniales_Heterocapsaceae_Heterocapsa_triquetra_N/A 99 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_ostenfeldii_N/A 100 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_catenella_OF101 100 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_andersonii_CCMP2222 100 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_minutum_CCMP113 81 100 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_minutum_N/A 40 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_catenella_N/A 100 100 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_fundyense_CCMP1719 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_tamarense_N/A 100 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_tamarense_CCMP1771 100 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_margalefii_AMGDE01CS-322 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Alexandrium_monilatum_CCMP3105 100 100 100 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Goniodomataceae_Pyrodinium_bahamense_pbaha01 99 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Goniodomataceae_Gambierdiscus_australes_CAWD149 100 99 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Gonyaulax_spinifera_CCMP409 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Gonyaulacaceae_Protoceratium_reticulatum_CCCM535EqCCMP1889 99 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_N/A_Lingulodinium_polyedrum_CCMP1738 70 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Ceratiaceae_Neoceratium_fusus_PA161109 100 Alveolata_Dinophyta_Dinophyceae_Peridiniales_Podolampaceae_Lessardia_elongata_SPMC104 100 Alveolata_Dinophyta_Dinophyceae_Gonyaulacales_Amphidomataceae_Azadinium_spinosum_3D9 Alveolata_Dinophyta_Dinophyceae_Dinophysiales_Dinophysiaceae_Dinophysis_acuminata_DAEP01 100 Alveolata_Dinophyta_Dinophyceae_Gymnodiniales_Gymnodiniaceae_Gymnodinium_catenatum_GC744 Alveolata_Dinophyta_Dinophyceae_Gymnodiniales_Gymnodiniaceae_Togula_jolla_CCCM725 61 Alveolata_Dinophyta_Dinophyceae_Gymnodiniales_Kareniaceae_Karenia_brevis_Wilson 100 100 100 Alveolata_Dinophyta_Dinophyceae_Gymnodiniales_Kareniaceae_Karenia_brevis_SP1 100 Alveolata_Dinophyta_Dinophyceae_Gymnodiniales_Kareniaceae_Karenia_brevis_CCMP2229 Alveolata_Dinophyta_Dinophyceae_Gymnodiniales_Kareniaceae_Karenia_brevis_SP3 100 100 Alveolata_Dinophyta_Dinophyceae_Gymnodiniales_Kareniaceae_Karlodinium_veneficum_N/A 100 Alveolata_Dinophyta_Dinophyceae_Gymnodiniales_Kareniaceae_Karlodinium_veneficum_CCMP2283 100 Alveolata_Dinophyta_Dinophyceae_Gymnodiniales_Gymnodiniaceae_Amphidinium_massartii_CS-259 100 Alveolata_Dinophyta_Dinophyceae_Gymnodiniales_Gymnodiniaceae_Amphidinium_carterae_CCMP1314 100Alveolata_Dinophyta_Dinophyceae_Noctilucales_Noctilucaceae_Noctiluca_scintillans_N/A 100 Alveolata_Dinophyta_Dinophyceae_Syndiniales_Amoebophryaceae_Amoebophrya_sp_Ameob2 Alveolata_Dinophyta_Dinophyceae_Syndiniales_Amoebophryaceae_Amoebophrya_sp_js026 100 Alveolata_Dinophyta_Dinophyceae_N/A_N/A_N/A_N/A_MALV2 100 100 Alveolata_Dinophyta_Dinophyceae_Syndiniales_Syndiniaceae_Hematodinium_sp_SG-2015 81 Alveolata_Dinophyta_Dinophyceae_Syndiniales_Syndiniaceae_Hematodinium_sp_N/A 98 Alveolata_Dinophyta_Dinophyceae_Oxyrrhinales_Oxyrrhinaceae_Oxyrrhis_marina_CCMP1795 100 100 Alveolata_Dinophyta_Dinophyceae_Oxyrrhinales_Oxyrrhinaceae_Oxyrrhis_marina_LB1974 100 Alveolata_Dinophyta_Dinophyceae_Oxyrrhinales_Oxyrrhinaceae_Oxyrrhis_marina_N/A Alveolata_Dinophyta_Dinophyceae_Oxyrrhinales_Oxyrrhinaceae_Oxyrrhis_marina_js006 Alveolata_Dinophyta_Dinophyceae_N/A_N/A_Psammosa_pacifica_N/A 100 Alveolata_Perkinsozoa_N/A_Perkinsida_Perkinsidae_Perkinsus_chesapeaki_ATCCPRA-65 Alveolata_Perkinsozoa_N/A_Perkinsida_Perkinsidae_Perkinsus_marinus_N/A100 100 Alveolata_Apicomplexa_Aconoidasida_Haemosporida_Plasmodiidae_Plasmodium_chabaudi_N/A 100 Alveolata_Apicomplexa_Aconoidasida_Haemosporida_Plasmodiidae_Plasmodium_chabaudi_PCHAS01 86 Alveolata_Apicomplexa_Aconoidasida_Haemosporida_Plasmodiidae_Plasmodium_yoelii_N/A Alveolata_Apicomplexa_Aconoidasida_Haemosporida_Plasmodiidae_Plasmodium_berghei_N/A 100 100 Alveolata_Apicomplexa_Aconoidasida_Haemosporida_Plasmodiidae_Plasmodium_vivax_N/A Alveolata_Apicomplexa_Aconoidasida_Haemosporida_Plasmodiidae_Plasmodium_knowlesi_N/A 100 Alveolata_Apicomplexa_Aconoidasida_Haemosporida_Plasmodiidae_Plasmodium_falciparum_Plas_falc_7G8_V1 Alveolata_Apicomplexa_Aconoidasida_Haemosporida_Plasmodiidae_Plasmodium_falciparum_N/A 100 100 100 Alveolata_Apicomplexa_Aconoidasida_N/A_Theileriidae_Theileria_parva_N/A 100 100 Alveolata_Apicomplexa_Aconoidasida_N/A_Theileriidae_Theileria_annulata_N/A 100 Alveolata_Apicomplexa_Aconoidasida_N/A_Theileriidae_Theileria_orientalis_ASM74089v1 100 Alveolata_Apicomplexa_Aconoidasida_N/A_Theileriidae_Theileria_equi_JCVI-bewag-v1.1 100 100 Alveolata_Apicomplexa_Aconoidasida_N/A_Babesiidae_Babesia_bigemina_Bbig001 Alveolata_Apicomplexa_Aconoidasida_N/A_Babesiidae_Babesia_bovis_N/A 100 Alveolata_Apicomplexa_Aconoidasida_N/A_Babesiidae_Babesia_microti_N/A 100 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Sarcocystidae_Hammondia_hammondi_HHA1_v02 100 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Sarcocystidae_Toxoplasma_gondii_N/A 100 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Sarcocystidae_Neospora_caninum_N/A 100 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Eimeriidae_Eimeria_tenella_N/A 34 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Eimeriidae_Eimeria_tenella_ETH001 100 Alveolata_Apicomplexa_Gregarinasina_Eugregarinorida_Lecudinidae_Ascogregarina_taiwanensis_N/A Alveolata_Apicomplexa_Gregarinasina_Eugregarinorida_Gregarinidae_Gregarina_niphandrodes_GNI3 98 Alveolata_Apicomplexa_Gregarinasina_Eugregarinorida_Lecudinidae_Lankesteria_abbotti_GrapplerInletBC100 100 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Cryptosporidiidae_Cryptosporidium_parvum_N/A 100 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Cryptosporidiidae_Cryptosporidium_hominis_N/A 51 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Cryptosporidiidae_Cryptosporidium_muris_N/A 100 Alveolata_Chrompodelida_N/A_N/A_N/A_Voromonas_pontica_N/A 100Alveolata_Chrompodelida_N/A_N/A_N/A_Voromonas_pontica_GG 100 Alveolata_Chrompodelida_N/A_N/A_Colpodellidae_Colpodella_sp_N/A Alveolata_Chrompodelida_N/A_N/A_Colpodellidae_Colpodella_angusta_N/A 100 100 Alveolata_Chrompodelida_N/A_N/A_N/A_Chromera_velia_N/A 100 Alveolata_Chrompodelida_N/A_N/A_N/A_Chromera_velia_CCMP2878 100 Alveolata_Chrompodelida_N/A_N/A_Colpodellidae_Colpodella_edax_N/A 100 Alveolata_Chrompodelida_N/A_N/A_N/A_Vitrella_brassicaformis_Vbrassicaformis Alveolata_Chrompodelida_N/A_N/A_N/A_Vitrella_brassicaformis_CCMP3155100 100 Alveolata_Ciliophora_Spirotrichea_Tintinnida_Xystonellidae_Favella_ehrenbergii_Fehren1 100 Alveolata_Ciliophora_Spirotrichea_Tintinnida_Rhabdonellidae_Schmidingerella_taraikaensis_FeNarragansettBay 100 Alveolata_Ciliophora_Spirotrichea_Choreotrichida_Strombidinopsidae_Strombidinopsis_sp_SopsisLIS2011 Alveolata_Ciliophora_Spirotrichea_Choreotrichida_Strombidinopsidae_Strombidinopsis_acuminatum_SPMC142 100 Alveolata_Ciliophora_Spirotrichea_N/A_Strombidiidae_Strombidium_inclinatum_S3 100 100 Alveolata_Ciliophora_Spirotrichea_N/A_Strombidiidae_Strombidium_rassoulzadegani_ras09 100 Alveolata_Ciliophora_Spirotrichea_Sporadotrichida_Oxytrichidae_Oxytricha_trifallax_oxytricha_asm_v1.1 100 Alveolata_Ciliophora_Spirotrichea_Sporadotrichida_Oxytrichidae_Sterkiella_histriomuscorum_N/A 100 100 Alveolata_Ciliophora_Spirotrichea_Sporadotrichida_Oxytrichidae_Stylonychia_lemnae_Stylonychia_lemnae_asm_v1.0 100 Alveolata_Ciliophora_Spirotrichea_Urostylida_Pseudokeronopsidae_Pseudokeronopsis_sp_OXSARD2 100 100 Alveolata_Ciliophora_Spirotrichea_Urostylida_Pseudokeronopsidae_Pseudokeronopsis_sp_Brazil 100 Alveolata_Ciliophora_Spirotrichea_Euplotida_Euplotidae_Euplotes_focardii_TN1 Alveolata_Ciliophora_Spirotrichea_Euplotida_Euplotidae_Moneuplotes_crassus_CT5 Alveolata_Ciliophora_Spirotrichea_Euplotida_Euplotidae_Euplotes_harpa_FSP1.4 100 Alveolata_Ciliophora_Litostomatea_Pleurostomatida_Litonotidae_Litonotus_pictus_P1 100 100 100 Alveolata_Ciliophora_Oligohymenophorea_Philasterida_Orchitophryidae_Anophryoides_haemophila_AH6_2 Alveolata_Ciliophora_Oligohymenophorea_Philasterida_Orchitophryidae_Anophryoides_haemophila_AH6_1 100 Alveolata_Ciliophora_Oligohymenophorea_Philasterida_Pseudocohnilembidae_Pseudocohnilembus_persalinus_ASM144751v1 100 100 97 Alveolata_Ciliophora_Oligohymenophorea_Hymenostomatida_Tetrahymenidae_Tetrahymena_thermophila_N/A 100 Alveolata_Ciliophora_Oligohymenophorea_Hymenostomatida_N/A_Ichthyophthirius_multifiliis_N/A Alveolata_Ciliophora_Oligohymenophorea_Peniculida_Parameciidae_Paramecium_tetraurelia_N/A 100 Alveolata_Ciliophora_Oligohymenophorea_N/A_N/A_Aristerostoma_sp_ATCC50986 Alveolata_Ciliophora_Colpodea_Cyrtolophosidida_Platyophryidae_Platyophrya_macrostoma_WH 100 100 Alveolata_Ciliophora_Spirotrichea_N/A_N/A_Protocruzia_adherens_Boccale 100 Alveolata_Ciliophora_Heterotrichea_Heterotrichida_Blepharismidae_Blepharisma_japonicum_StockR1072 100 Alveolata_Ciliophora_Heterotrichea_Heterotrichida_Fabreidae_Fabrea_salina_js003 67 Alveolata_Ciliophora_Heterotrichea_Heterotrichida_Condylostomatidae_Condylostoma_magnum_COL2 97 Alveolata_Ciliophora_Heterotrichea_Heterotrichida_Climacostomidae_Climacostomum_virens_StockW-24 Alveolata_Ciliophora_Heterotrichea_N/A_N/A_N/A_N/A_js008 99 Alveolata_Ciliophora_Litostomatea_Cyclotrichida_Mesodiniidae_Mesodinium_pulex_SPMC105 100 Alveolata_Ciliophora_Litostomatea_Cyclotrichida_Mesodiniidae_Myrionecta_rubra_CCMP2563 100 Alveolata_Colponemidia_N/A_N/A_N/A_N/A_N/A_Colp15 99 Alveolata_Colponemidia_N/A_N/A_N/A_N/A_N/A_Colp10 Alveolata_Colponemidia_N/A_N/A_N/A_Colponema_vietnamica_N/A Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gigartinales_Furcellariaceae_Furcellaria_lumbricalis_N/A52 41 Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Bolivinitidae_Brizalina_sp_N/A 100 Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Buliminidae_Globobulimina_turgida_N/A 71 Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Nonionidae_Nonionellina_sp_N/A 100 Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Nonionidae_Nonionellina_sp_SRR2003403 90 37 Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Buliminidae_Bulimina_marginata_SRR2003397 Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Buliminidae_Bulimina_marginata_N/A 86 Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Elphidiidae_Elphidium_sp_N/A 87 Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Rosalinidae_Rosalina_sp_N/A 96 Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Rotaliidae_Ammonia_sp_N/A 100 Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Elphidiidae_Elphidium_margaritaceum_N/A Rhizaria_Retaria-Foraminifera_N/A_Rotaliida_Bolivinitidae_Brizalina_sp_SRR2003388 100 100 Rhizaria_Retaria-Foraminifera_N/A_Miliolida_Miliolidae_Quinqueloculina_sp_N/A Rhizaria_Retaria-Foraminifera_N/A_Miliolida_Soritidae_Sorites_sp_N/A 100 Rhizaria_Retaria-Foraminifera_N/A_N/A_Reticulomyxidae_Reticulomyxa_filosa_N/A 100 Rhizaria_Retaria-Radiolaria_Polycystinea_Spumellaria_Actinommidae_Spongosphaera_streptacantha_N/A 100 Rhizaria_Retaria-Radiolaria_Polycystinea_Spumellaria_Actinommidae_Spongosphaera_streptacantha_SRR1734679 100 100 Rhizaria_Retaria-Radiolaria_Polycystinea_Collodaria_Sphaerozoidae_Collozoum_sp_N/A 100 Rhizaria_Retaria-Radiolaria_Polycystinea_Collodaria_Sphaerozoidae_Collozoum_sp_SRR1744093 100 Rhizaria_Retaria-Radiolaria_Acantharea_Arthracanthida_Acanthometridae_Amphilonche_elongata_SRR1734678 99 100 Rhizaria_Retaria-Radiolaria_Acantharea_Arthracanthida_Acanthometridae_Amphilonche_elongata_N/A Rhizaria_Retaria-Radiolaria_Acantharea_Arthracanthida_Phyllostauridae_Phyllostaurus_siculus_N/A 100 Rhizaria_Retaria-Radiolaria_Acantharea_Symphyacanthida_Astrolithidae_Astrolonche_serrata_N/A 100 Rhizaria_Apofilosa_N/A_N/A_Gromiidae_Gromia_sphaerica_SRR2003399 55 Rhizaria_Apofilosa_N/A_N/A_Gromiidae_Gromia_sphaerica_N/A 100 Rhizaria_Apofilosa_N/A_N/A_N/A_Corallomyxa_sp_N/A 60 100 Rhizaria_Phytorhiza_N/A_N/A_Plasmodiophoridae_Plasmodiophora_brassicae_N/A 100 Rhizaria_Phytorhiza_N/A_N/A_Plasmodiophoridae_Plasmodiophora_brassicae_pbe3.h15 Rhizaria_Phytorhiza_N/A_N/A_Plasmodiophoridae_Spongospora_subterranea_N/A Rhizaria_Phytorhiza_N/A_Vampyrellida_Leptophryidae_Leptophrys_vorax_SRR2003407 Rhizaria_N/A_N/A_N/A_N/A_N/A_N/A_Lapot_cDNA100 100 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Bigelowiella_longifila_CCMP242 100 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Bigelowiella_natans_N/A Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Norrisiella_sphaerica_BC52 89 100 100 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Chlorarachnion_reptans_CCCM449 88 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Amorphochlora_amoebiformis_CCMP2058 100 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Gymnochlora_sp_CCMP2014 100 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Partenskyella_glossopodia_RCC365 97 100 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Lotharella_globosa_CCCM811 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Lotharella_globosa_LEX01 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Lotharella_oceanica_CCMP622 72 Rhizaria_Filosa_N/A_N/A_Guttulinaceae_Guttulinopsis_vulgaris_N/A 100 100 Rhizaria_Filosa_N/A_Euglyphida_Paulinellidae_Paulinella_chromatophora_CCAC0185 100 Rhizaria_Filosa_N/A_Euglyphida_Euglyphidae_Euglypha_rotunda_SRR2006120 Rhizaria_Filosa_N/A_Euglyphida_Paulinellidae_Paulinella_chromatophora_N/A 100 100 Rhizaria_Filosa_N/A_Cercomonadida_Cercomonadidae_Paracercomonas_marina_N/A 96 100 Rhizaria_Filosa_N/A_Phaeocystida_Aulacanthidae_Aulacantha_scolymantha_SRR1734688 Rhizaria_Filosa_N/A_Phaeocystida_Aulacanthidae_Aulacantha_scolymantha_N/A Rhizaria_N/A_N/A_N/A_N/A_N/A_N/A_D1 100 Rhizaria_Filosa_N/A_Cercomonadida_Cercomonadidae_Massisteria_sp_N/A 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Chlamydomonadaceae_Chlamydomonas_leiostraca_SAG11-49 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Chlamydomonadaceae_Chlamydomonas_sp_CCMP681 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Dunaliellaceae_Dunaliella_tertiolecta_CCMP1320 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Chlamydomonadaceae_Chlamydomonas_chlamydogama_SAG11-48b 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Chlamydomonadaceae_Chlamydomonas_euryale_CCMP219 94 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Volvocaceae_Volvox_carteri_N/A Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Chlamydomonadaceae_Chlamydomonas_reinhardtii_N/A Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Chlamydomonadaceae_Polytomella_parva_SAG63-3 94 100 Archaeplastida-Viridiplantae_Chlorophyta_Ulvophyceae_Dasycladales_Polyphysaceae_Acetabularia_acetabulum_js009 100 Archaeplastida-Viridiplantae_Chlorophyta_Trebouxiophyceae_N/A_N/A_Picochlorum_oklahomense_CCMP2329 100 Archaeplastida-Viridiplantae_Chlorophyta_Trebouxiophyceae_N/A_N/A_Picochlorum_sp_RCC944 100 Archaeplastida-Viridiplantae_Chlorophyta_Trebouxiophyceae_Chlorellales_N/A_Helicosporidium_sp_ATCC50920 100 Archaeplastida-Viridiplantae_Chlorophyta_Trebouxiophyceae_Chlorellales_Chlorellaceae_Chlorella_vulgaris_N/A 100 Archaeplastida-Viridiplantae_Chlorophyta_Trebouxiophyceae_Microthamniales_N/A_Stichococcus_sp_RCC1054 Archaeplastida-Viridiplantae_Chlorophyta_Trebouxiophyceae_N/A_Coccomyxaceae_Coccomyxa_sp_N/A 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorodendrophyceae_Chlorodendrales_Chlorodendraceae_Tetraselmis_striata_LANL1001 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorodendrophyceae_Chlorodendrales_Chlorodendraceae_Tetraselmis_chuii_PLY429 99 Archaeplastida-Viridiplantae_Chlorophyta_Chlorodendrophyceae_Chlorodendrales_Chlorodendraceae_Tetraselmis_astigmatica_CCMP880 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorodendrophyceae_Chlorodendrales_Chlorodendraceae_Tetraselmis_sp_GSL018100 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_N/A_N/A_N/A_RCC2335 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_Pycnococcaceae_Pycnococcus_sp_CCMP1998 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_N/A_N/A_N/A_RCC1871 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_N/A_N/A_N/A_CCMP1205 64 100 100 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_N/A_N/A_N/A_RCC701 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_N/A_N/A_N/A_RCC856 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_N/A_N/A_N/A_RCC998 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_N/A_N/A_N/A_CCMP2111 98 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_N/A_N/A_N/A_RCC2339 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_N/A_Picocystis_salinarum_CCMP189790 100Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_Pycnococcaceae_Pycnococcus_provasolii_RCC931 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_Pycnococcaceae_Pycnococcus_provasolii_RCC251 64 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_Pycnococcaceae_Pycnococcus_provasolii_RCC2336 Archaeplastida-Viridiplantae_Chlorophyta_N/A_N/A_Pycnococcaceae_Pycnococcus_provasolii_RCC733 Archaeplastida-Viridiplantae_Chlorophyta_Nephroselmidophyceae_N/A_N/A_Nephroselmis_pyriformis_CCMP717100 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Micromonas_pusilla_CCMP1723 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Micromonas_sp_RCC472 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Micromonas_pusilla_CCMP494 76 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Micromonas_sp_N/A 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Micromonas_sp_NEPCC29 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Micromonas_pusilla_RCC1614 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Micromonas_pusilla_N/A 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Micromonas_sp_CCMP2099 100 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Micromonas_pusilla_RCC2306 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Micromonas_pusilla_CCAC1681 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Mantoniella_sp_CCMP1436 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_Mantoniella_antarctica_SL-175 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Mamiellaceae_N/A_N/A_RCC2288100 94 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Ostreococcus_mediterraneus_clade-D-RCC2593 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Ostreococcus_mediterraneus_clade-D-RCC1621 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Ostreococcus_mediterraneus_clade-D-RCC2596 100 62 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Ostreococcus_mediterraneus_clade-D-RCC1107 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Ostreococcus_mediterraneus_clade-D-RCC2573 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Ostreococcus_mediterraneus_clade-D-RCC2572 100 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Ostreococcus_lucimarinus_clade-A-BCC118000 100 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Ostreococcus_lucimarinus_N/A 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Ostreococcus_tauri_N/A 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Bathycoccus_prasinos_BCC99000 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Bathycoccus_prasinos_CCMP1898 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Mamiellales_Bathycoccaceae_Bathycoccus_prasinos_RCC716 100 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Dolichomastigales_Crustomastigaceae_Crustomastix_stigmatica_CCMP3273 Archaeplastida-Viridiplantae_Chlorophyta_Mamiellophyceae_Dolichomastigales_Dolichomastigaceae_Dolichomastix_tenuilepis_CCMP3274 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Pyramimonadales_N/A_Pyramimonas_sp_CCMP2087 100 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Pyramimonadales_N/A_Pyramimonas_obovata_CCMP722 100 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Pyramimonadales_N/A_Pyramimonas_parkeae_CCMP726 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Pyramimonadales_N/A_Polyblepharides_amylifera_CCMP720 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Pyramimonadales_N/A_Pterosperma_sp_CCMP1384 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Prasinococcales_N/A_Prasinoderma_singulare_RCC927 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Prasinococcales_N/A_Prasinoderma_coloniale_CCMP1413 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Prasinococcales_N/A_Prasinococcus_capsulatus_CCMP1194100 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Brassicales_Brassicaceae_Arabidopsis_thaliana_N/A Archaeplastida-Viridiplantae_Streptophyta_N/A_Brassicales_Brassicaceae_Arabidopsis_lyrata_N/A 99 Archaeplastida-Viridiplantae_Streptophyta_N/A_Brassicales_Brassicaceae_Arabidopsis_thaliana_TAIR10 100100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Malpighiales_Euphorbiaceae_Ricinus_communis_N/A 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Malpighiales_Salicaceae_Populus_trichocarpa_N/A 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Fabales_Fabaceae_Glycine_max_N/A Archaeplastida-Viridiplantae_Streptophyta_N/A_Lamiales_Phrymaceae_Erythranthe_guttata_N/A 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Vitales_Vitaceae_Vitis_vinifera_N/A 100 66 Archaeplastida-Viridiplantae_Streptophyta_N/A_Vitales_Vitaceae_Vitis_vinifera_IGGP_12x100 100 Archaeplastida-Viridiplantae_Streptophyta_Liliopsida_Poales_Poaceae_Zea_mays_AGPv4 Archaeplastida-Viridiplantae_Streptophyta_Liliopsida_Poales_Poaceae_Zea_mays_N/A 100 100 100 Archaeplastida-Viridiplantae_Streptophyta_Liliopsida_Poales_Poaceae_Sorghum_bicolor_N/A 94 Archaeplastida-Viridiplantae_Streptophyta_Liliopsida_Poales_Poaceae_Hordeum_vulgare_N/A Archaeplastida-Viridiplantae_Streptophyta_Liliopsida_Poales_Poaceae_Brachypodium_distachyon_N/A 100 Archaeplastida-Viridiplantae_Streptophyta_Liliopsida_Poales_Poaceae_Oryza_sativa_N/A 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Chloranthales_Chloranthaceae_Sarcandra_glabra_js024 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Laurales_Lauraceae_Persea_americana_js020 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Amborellales_Amborellaceae_Amborella_trichopoda_AMTR1.0 100 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Welwitschiales_Welwitschiaceae_Welwitschia_mirabilis_js025 Archaeplastida-Viridiplantae_Streptophyta_N/A_Pinales_Pinaceae_Pinus_taeda_js021 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Ginkgoales_Ginkgoaceae_Ginkgo_biloba_js014 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Polypodiales_Dennstaedtiaceae_Pteridium_aquilinum_js023 99 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Psilotales_Psilotaceae_Psilotum_nudum_js022 100 Archaeplastida-Viridiplantae_Streptophyta_N/A_Selaginellales_Selaginellaceae_Selaginella_moellendorffii_N/A 99 100 Archaeplastida-Viridiplantae_Streptophyta_Bryopsida_Funariales_Funariaceae_Physcomitrella_patens_N/A Archaeplastida-Viridiplantae_Streptophyta_Marchantiopsida_Marchantiales_Marchantiaceae_Marchantia_polymorpha_js016 100 Archaeplastida-Viridiplantae_Streptophyta_Anthocerotopsida_Dendrocerotales_Dendrocerotaceae_Nothoceros_aenigmaticus_js019 100 Archaeplastida-Viridiplantae_Streptophyta_Zygnemophyceae_Zygnematales_Zygnemataceae_Netrium_digitus_js018 100 Archaeplastida-Viridiplantae_Streptophyta_Zygnemophyceae_Zygnematales_Mesotaeniaceae_Cylindrocystis_brebissonii_js013 100 Archaeplastida-Viridiplantae_Streptophyta_Coleochaetophyceae_Coleochaetales_Coleochaetaceae_Coleochaete_scutata_js012 100 Archaeplastida-Viridiplantae_Streptophyta_Charophyceae_Charales_Characeae_Chara_vulgaris_js011 Archaeplastida-Viridiplantae_Streptophyta_Klebsormidiophyceae_Klebsormidiales_Klebsormidiaceae_Klebsormidium_subtile_js015 100 Archaeplastida-Viridiplantae_Streptophyta_Mesostigmatophyceae_Mesostigmatales_Mesostigmataceae_Mesostigma_viride_js017 100 Archaeplastida-Viridiplantae_Streptophyta_Mesostigmatophyceae_Mesostigmatales_Mesostigmataceae_Mesostigma_viride_N/A 100 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_Gloeochaetales_Gloeochaetaceae_Gloeochaete_wittrockiana-ARP_SAG46.84 85 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_Gloeochaetales_Gloeochaetaceae_Gloeochaete_wittrockiana_SAG46.84 100 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_Glaucocystales_Glaucocystaceae_Glaucocystis_nostochinearum_N/A Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_Cyanophoraceae_Cyanophora_paradoxa_N/A Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_N/A_Cyanoptyche_gloeocystis_SAG4.97100 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Geminigera_sp_CaronLabIsolate Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Geminigera_sp_js004 98 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Geminigera_cryophila_CCMP2564 100 96 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Cryptomonadaceae_Plagioselmis_nannoplanctica_N/A 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Teleaulax_amphioxeia_SRR4098290 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Cryptomonadaceae_Plagioselmis_sp_N/A 100 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Guillardia_theta_N/A 72 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Hanusia_phi_CCMP325 100 Cryptista_Cryptophyta_Cryptophyta_N/A_N/A_Cryptophyceae_sp_CCMP2293 100 65 Cryptista_Cryptophyta_Cryptophyta_N/A_N/A_Cryptophyceae_sp_N/A 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Pyrenomonadaceae_Rhodomonas_salina_N/A 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Pyrenomonadaceae_Rhodomonas_salina_CCMP1319 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Pyrenomonadaceae_Rhodomonas_lens_RHODO 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Pyrenomonadaceae_Rhodomonas_sp_CCMP768 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Pyrenomonadaceae_Rhodomonas_abbreviata_CaronLabIsolate 100 97Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Proteomonas_sulcata_CCMP704 98 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Hemiselmidaceae_Hemiselmis_andersenii_CCMP441 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Hemiselmidaceae_Hemiselmis_andersenii_CCMP1180 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Hemiselmidaceae_Hemiselmis_andersenii_CCMP439 100 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Hemiselmidaceae_Hemiselmis_andersenii_CCMP644 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Hemiselmidaceae_Hemiselmis_tepida_CCMP443 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Hemiselmidaceae_Hemiselmis_rufescens_PCC563 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Hemiselmidaceae_Hemiselmis_virescens_PCC157 96 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Chroomonadaceae_Chroomonas_mesostigmatica_CCMP1168 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Cryptomonadaceae_Cryptomonas_paramecium_CCAP977_2a Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Cryptomonadaceae_Cryptomonas_curvata_CCAP979_52 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_pacifica_N/A 35 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_pacifica_CCMP1869 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_sp_m 91 74 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_avonlea_N/A 30 Cryptista_Katablepharida_Katablepharidophyta_N/A_N/A_N/A_N/A_38W Cryptista_Katablepharida_Katablepharidophyta_N/A_N/A_Roombia_truncata_N/A 100 Cryptista_Katablepharida_Katablepharidophyta_N/A_N/A_N/A_N/A_11W Cryptista_Katablepharida_Katablepharidophyta_N/A_N/A_N/A_N/A_17W 100 Cryptista_Palpitia_N/A_N/A_N/A_Palpitomonas_bilix_NIES-2562 Cryptista_Palpitia_N/A_N/A_N/A__Palpitomonas_bilix_N/A100 100 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gracilariales_Gracilariaceae_Gracilaria_changii_N/A 100 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gracilariales_Gracilariaceae_Gracilaria_sp_N/A 100 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gracilariales_Gracilariaceae_Gracilariopsis_chorda_N/A Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Ceramiales_Ceramiaceae_Griffithsia_okiensis_N/A 100 100 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gigartinales_Solieriaceae_Eucheuma_denticulatum_N/A 99 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gigartinales_Gigartinaceae_Chondrus_crispus_N/A 100 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Corallinales_Corallinaceae_Calliarthron_tuberculosum_N/A Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Palmariales_Palmariaceae_Palmaria_palmata_Weber_Mohr 100 100 100 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Hildenbrandiales_Hildenbrandiaceae_Hildenbrandia_rubra_UTEX2621 100 Archaeplastida-Rhodophyta_Rhodophyta_Bangiophyceae_Bangiales_Bangiaceae_Porphyra_umbilicalis_N/A 48 100 Archaeplastida-Rhodophyta_Rhodophyta_Bangiophyceae_Bangiales_Bangiaceae_Porphyra_umbilicalis_4086291 Archaeplastida-Rhodophyta_Rhodophyta_Bangiophyceae_Bangiales_Bangiaceae_Porphyra_purpurea_N/A Archaeplastida-Rhodophyta_Rhodophyta_Bangiophyceae_Bangiales_Bangiaceae_Pyropia_yezoensis_N/A Archaeplastida-Rhodophyta_Rhodophyta_Rhodellophyceae_Rhodellales_Rhodellaceae_Rhodella_violacea_CCMP736 78 100 100 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Erythrolobus_madagascarensis_CCMP3276 100 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Erythrolobus_australicus_CCMP3124 100 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Timspurckia_oligopyrenoides_CCMP3278 65 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Porphyridium_aerugineum_SAG1380-2 100 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Porphyridium_purpureum_N/A 58 100 Archaeplastida-Rhodophyta_Rhodophyta_Compsopogonophyceae_Rhodochaetales_Rhodochaetaceae_Rhodochaete_pulchella_CCMP3232 Archaeplastida-Rhodophyta_Rhodophyta_Compsopogonophyceae_Erythropeltidales_Erythrotrichiaceae_Madagascaria_erythrocladoides_CCMP3234 100 Archaeplastida-Rhodophyta_Rhodophyta_Compsopogonophyceae_Compsopogonales_Compsopogonaceae_Compsopogon_caeruleus_SAG36.94 100 Archaeplastida-Rhodophyta_Rhodophyta_Stylonematophyceae_Stylonematales_Stylonemataceae_Purpureofilum_apyrenoidigerum_CCMP3233 100 Archaeplastida-Rhodophyta_Rhodophyta_Stylonematophyceae_Stylonematales_Stylonemataceae_N/A_N/A_CCMP1999 50 Archaeplastida-Rhodophyta_Rhodophyta_Stylonematophyceae_Stylonematales_Stylonemataceae_Rhodosorus_marinus_UTEXLB2760 Archaeplastida-Rhodophyta_Rhodophyta_Stylonematophyceae_Stylonematales_Stylonemataceae_Rhodosorus_marinus_CCMP769 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Cryptomonadaceae_Cryptomonas_paramecium_ASM19445v1 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Chroomonadaceae_Chroomonas_mesostigmatica_ASM28609v1 100 95 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Pyrenomonadaceae_Rhodomonas_sp-nucleomorph_CCMP768 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Pyrenomonadaceae_Rhodomonas_salina-nucleomorph_N/A 94 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Guillardia_theta-nucleomorph_N/A 86 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Geminigera_cryophila-nucleomorph_CCMP2564 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Teleaulax_amphioxeia-nucleomorph_SRR4098290 89 66 Cryptista_Cryptophyta_Cryptophyta_N/A_N/A_Cryptophyceae_sp-nucleomorph_CCMP2293 Cryptista_Cryptophyta_Cryptophyta_N/A_N/A_Cryptophyceae_sp-nucleomorph_N/A 100 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Cryptomonadaceae_Cryptomonas_paramecium-nucleomorph_ASM19445v1 83 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Cryptomonadaceae_Cryptomonas_paramecium-nucleomorph_N/A 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Chroomonadaceae_Chroomonas_mesostigmatica-nucleomorph_ASM28609v1 28 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Chroomonadaceae_Chroomonas_mesostigmatica-nucleomorph_N/A 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Hemiselmidaceae_Hemiselmis_andersenii-nucleomorph_N/A 94 Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Cyanidium_caldarium_Tilden_Geitler Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Cyanidioschyzon_merolae_N/A 100 Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Galdieria_sulphuraria_N/A 100 Rhodophyta-sister_N/A_N/A_N/A_N/A_N/A_N/A_Colp29 100 Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_marinus_N/A Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_limneticus_N/A100 45 Picozoa_Picozoa_N/A_N/A_N/A_Picobiliphyte_sp_MS584-11 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_COSAG05 100 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_SAG33 100 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_COSAG01 100 100 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_SAG25 100 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_COSAG03 100 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_COSAG02 100 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_COSAG06 89 63 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_COSAG04 100 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_SAG22 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_SAG11 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_SAG31 59 Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_PLYM219 78 Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_379 8699 Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_CCMP370 100 Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_374 100 Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_N/A Haptista_Haptophyta_N/A_Isochrysidales_Isochrysidaceae_Isochrysis_sp_CCMP1244 100 100 Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Gephyrocapsa_oceanica_RCC1303 100 Haptista_Haptophyta_N/A_Isochrysidales_Isochrysidaceae_Isochrysis_galbana_N/A Haptista_Haptophyta_N/A_Isochrysidales_Isochrysidaceae_Isochrysis_galbana_CCMP1323 100 100 Haptista_Haptophyta_N/A_Isochrysidales_Isochrysidaceae_Isochrysis_sp_CCMP1324 100 Haptista_Haptophyta_N/A_Coccolithales_Coccolithaceae_Coccolithus_braarudii_N/A 100 Haptista_Haptophyta_N/A_Coccolithales_Coccolithaceae_Coccolithus_pelagicus_PLY182g 100 Haptista_Haptophyta_N/A_Coccolithales_Calcidiscaceae_Calcidiscus_leptoporus_RCC1130 Haptista_Haptophyta_N/A_Coccolithales_Pleurochrysidaceae_Pleurochrysis_carterae_CCMP645 Haptista_Haptophyta_N/A_Coccosphaerales_N/A_Scyphosphaera_apsteinii_RCC1455 100 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Prymnesium_parvum_N/A 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Prymnesium_parvum_Texoma1 100 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Prymnesium_polylepis_UIO037 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Prymnesium_polylepis_CCMP1757 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Haptolina_ericina_CCMP281 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Imantonia_rotunda_N/A 100 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Imantonia_sp_RCC918 100 Haptista_Haptophyta_N/A_Prymnesiales_Chrysochromulinaceae_Chrysochromulina_sp_CCMP291 Haptista_Haptophyta_N/A_Prymnesiales_Chrysochromulinaceae_Chrysochromulina_rotalis_UIO044 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Haptolina_brevifila_UTEXLB985 100 Haptista_Haptophyta_N/A_Phaeocystales_Phaeocystaceae_Phaeocystis_antarctica_CCMP1374 100 Haptista_Haptophyta_N/A_Phaeocystales_Phaeocystaceae_Phaeocystis_antarctica_CaronLabIsolate 100 Haptista_Haptophyta_N/A_Phaeocystales_Phaeocystaceae_Phaeocystis_sp_CCMP2710 100 Haptista_Haptophyta_N/A_Phaeocystales_Phaeocystaceae_Phaeocystis_rex_CCMP2000 Haptista_Haptophyta_N/A_Phaeocystales_Phaeocystaceae_Phaeocystis_cordata_RCC1383100 100 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_Pavlova_lutheri_N/A 100 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_Pavlova_lutheri_RCC1537 100 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_N/A_N/A_CCMP2436 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_Pavlovales_sp_N/A 100 100 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_Pavlova_sp_CCMP459 100 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_Pavlova_gyrans_CCMP608 89 Haptista_Haptophyta_N/A_N/A_N/A_Chrysoculter_rhomboideus_RCC1486 48 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_Exanthemachrysis_gayraliae_RCC1523 100 Haptista_Centrohelida_N/A_N/A_Raphidiophryidae_Raphidiophrys_heterophryoidea_N/A 57 Haptista_Centrohelida_N/A_N/A_Raphidiophryidae_Raphidiophrys_ambigua_N/A 97 Haptista_Centrohelida_N/A_N/A_Raphidiophryidae_Raphidiophrys_miako_N/A 100 Haptista_Centrohelida_N/A_N/A_Acanthocystidae_Raineriophrys_erinaceoides_N/A 88 Haptista_Centrohelida_N/A_N/A_Acanthocystidae_Acanthocystis_sp_N/A 89 Haptista_Centrohelida_N/A_N/A_Acanthocystidae_Choanocystis_sp_N/A100 100 Telonemia_N/A_N/A_Telonemida_N/A_Telonema_subtile_N/A 100 Telonemia_N/A_N/A_Telonemida_N/A_Telonema_subtile_Tel-1 Telonemia_N/A_N/A_Telonemida_N/A_N/A_N/A_P-1 100 Telonemia_N/A_N/A_Telonemida_N/A_N/A_N/A_P-2 100 Haptista-sister_N/A_N/A_N/A_N/A_N/A_N/A_colp32_S4 86 Haptista-sister_N/A_N/A_N/A_N/A_N/A_N/A_colp32_S3 Haptista-sister_N/A_N/A_N/A_N/A_Ancoracysta_twista_TD Hemimastigophora_N/A_N/A_N/A_Spironemidae_Hemimastix_kukwesjijk_N/A73 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Leishmania_major_ASM272v2 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Leishmania_infantum_N/A 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Leishmania_major_N/A 84 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Leptomonas_seymouri_ASM129953v1 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Leptomonas_pyrrhocoris_ASM129339v1 100 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Strigomonas_culicis_Strigomonas_culicis_Genome 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Angomonas_deanei_Angomonas_deanei_Genome 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Phytomonas_sp_AKI_PRJEB1539_v1 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Phytomonas_sp_AKH_PRJEB1535_v1 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Trypanosoma_rangeli_T_rangeli_SC58v1 100 100 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Trypanosoma_cruzi_N/A 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Trypanosoma_vivax_N/A Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Trypanosomatidae_Trypanosoma_brucei_N/A 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Bodonidae_Bodo_saltans_N/A 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Bodonidae_Procryptobia_sp_N/A 100 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Bodonidae_Neobodo_designis_CCAP1951_1 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_N/A_Perkinsela_sp_ASM123584v1 100 100 Excavata-Discoba_Euglenozoa_N/A_Diplonemida_N/A_Diplonema_papillatum_N/A 100 Excavata-Discoba_Euglenozoa_N/A_Euglenales_Euglenaceae_Euglena_longa_N/A Excavata-Discoba_Euglenozoa_N/A_Euglenales_Euglenaceae_Euglena_gracilis_N/A 100 Excavata-Discoba_Euglenozoa_N/A_Euglenales_Euglenaceae_Euglena_mutabilis_N/A 100 97 Excavata-Discoba_Euglenozoa_N/A_Eutreptiales_N/A_Eutreptiella_gymnastica_NIES-381 97 Excavata-Discoba_Euglenozoa_N/A_Eutreptiales_N/A_Eutreptiella_gymnastica_CCMP1594 98 Excavata-Discoba_Percolozoa_Heterolobosea_Schizopyrenida_Gruberellidae_Stachyamoeba_lipophora_N/A 99 Excavata-Discoba_Percolozoa_Heterolobosea_N/A_Psalteriomonadidae_Sawyeria_marylandensis_N/A 100 Excavata-Discoba_Percolozoa_Heterolobosea_Schizopyrenida_Vahlkampfiidae_Naegleria_gruberi_N/A 100 Excavata-Discoba_Percolozoa_Heterolobosea_N/A_N/A_Percolomonas_cosmopolitus_WS Excavata-Discoba_Percolozoa_Heterolobosea_N/A_N/A_Percolomonas_cosmopolitus_AE-1 100 Excavata-Discoba_N/A_N/A_N/A_Tsukubamonadidae_Tsukubamonas_globosa_N/A 70 Excavata-Discoba_Loukozoa_N/A_N/A_N/A_Seculamonas_ecuadoriensis_N/A 99 Excavata-Discoba_Loukozoa_N/A_N/A_Jakobidae_Jakoba_libera_N/A 100 100 Excavata-Discoba_Loukozoa_N/A_N/A_Histionidae_Histiona_aroides_N/A 100 Excavata-Discoba_Loukozoa_N/A_N/A_Histionidae_Reclinomonas_americana_N/A 69 Excavata-Discoba_Loukozoa_N/A_N/A_Jakobidae_Jakoba_bahamiensis_N/A Excavata-Discoba_N/A_Jakobida_Andalucina_Andaluciidae_Andalucia_godoyi_N/A 100 100 Excavata-Metamonada_Metamonada_N/A_N/A_Hexamitidae_Giardia_intestinalis_ASM18240v1 Excavata-Metamonada_Metamonada_N/A_N/A_Hexamitidae_Giardia_intestinalis_ASM49873v1 100 Excavata-Metamonada_Metamonada_N/A_N/A_Hexamitidae_Giardia_intestinalis_G_duodenalis_AssB_BAH15c1 100 100 Excavata-Metamonada_Metamonada_N/A_N/A_Hexamitidae_Giardia_intestinalis_ASM49871v1 100 100 Excavata-Metamonada_Metamonada_N/A_N/A_Hexamitidae_Giardia_intestinalis_N/A 100 Excavata-Metamonada_Metamonada_N/A_N/A_Hexamitidae_Spironucleus_salmonicida_SSK3.0 100 Excavata-Metamonada_Metamonada_N/A_Fornicata_Carpediemonas-like_Dysnectes_brevis_N/A Excavata-Metamonada_Metamonada_N/A_Fornicata_Retortamonadidae_Chilomastix_cuspidata_N/A 98 100 Excavata-Metamonada_Metamonada_N/A_Fornicata_Carpediemonas-like_Carpediemonas_membranifera_N/A 100 Opisthokonta-Fungi_Microsporidia_N/A_N/A_Nosematidae_Nosema_bombycis_NosBomCQ1_v1.0 99 Opisthokonta-Fungi_Microsporidia_N/A_N/A_Culicosporidae_Edhazardia_aedis_Edha_aedis_V4b Rhizaria_Ascetosporea_N/A_N/A_Mikrocytiidae_Mikrocytos_mackini_N/A 100 Excavata-Metamonada_Metamonada_N/A_Trichomonadida_Trichomonadidae_Trichomonas_vaginalis_N/A 100 Amoebozoa_Evosea_Archamoebae_N/A_N/A_Entamoeba_histolytica_N/A 100 Amoebozoa_Evosea_Archamoebae_N/A_N/A_Entamoeba_nuttalli_ENU1_v1 100 100 100 Amoebozoa_Evosea_Archamoebae_N/A_N/A_Entamoeba_dispar_N/A Amoebozoa_Evosea_Archamoebae_N/A_N/A_Entamoeba_dispar_JCVI_EDISG_1.0 100 Amoebozoa_Evosea_Archamoebae_N/A_N/A_Entamoeba_invadens_EIA2_v2 100 Excavata-Metamonada_Metamonada_N/A_N/A_N/A_Paratrimastix_pyriformis_js010 Excavata-Metamonada_Metamonada_N/A_N/A_N/A_Paratrimastix_pyriformis_N/A 100 Excavata-Metamonada_Metamonada_N/A_Oxymonadida_Polymastigidae_Monocercomonoides_sp_PA203 100 Opisthokonta-Metazoa_Arthropoda_Insecta_Diptera_Drosophilidae_Drosophila_melanogaster_BDGP6 100 Opisthokonta-Metazoa_Arthropoda_Insecta_Diptera_Culicidae_Culex_quinquefasciatus_CpipJ2 100 Opisthokonta-Metazoa_Arthropoda_Insecta_Coleoptera_Tenebrionidae_Tribolium_castaneum_Tcas3 100 Opisthokonta-Metazoa_Arthropoda_Insecta_Hymenoptera_Apidae_Apis_mellifera_GCA_000002195.1 Opisthokonta-Metazoa_Arthropoda_Insecta_Hemiptera_Aphididae_Acyrthosiphon_pisum_GCA_000142985.2 100 100 Opisthokonta-Metazoa_Arthropoda_Branchiopoda_Diplostraca_Daphniidae_Daphnia_pulex_N/A 100 Opisthokonta-Metazoa_Arthropoda_Arachnida_Ixodida_Ixodidae_Ixodes_scapularis_IscaW1 100 Opisthokonta-Metazoa_Arthropoda_Arachnida_Araneae_Eresidae_Stegodyphus_mimosarum_GCA_000611955.2 Opisthokonta-Metazoa_Arthropoda_Chilopoda_Geophilomorpha_Linotaeniidae_Strigamia_maritima_Smar1 100 Opisthokonta-Metazoa_Platyhelminthes_Cestoda_Cyclophyllidea_Taeniidae_Taenia_solium_Mexico 100 Opisthokonta-Metazoa_Platyhelminthes_Trematoda_Strigeidida_Schistosomatidae_Schistosoma_mansoni_ASM23792v2 100 100 Opisthokonta-Metazoa_Nematoda_Chromadorea_Diplogasterida_Neodiplogasteridae_Pristionchus_pacificus_P_pacificus-5.0 100 Opisthokonta-Metazoa_Nematoda_Chromadorea_Rhabditida_Rhabditidae_Caenorhabditis_elegans_WBcel235 100 Opisthokonta-Metazoa_Mollusca_Gastropoda_N/A_Lottiidae_Lottia_gigantea_N/A Opisthokonta-Metazoa_Mollusca_Bivalvia_Ostreoida_Ostreidae_Crassostrea_gigas_N/A 100 Opisthokonta-Metazoa_Mollusca_Cephalopoda_Octopoda_Octopodidae_Octopus_bimaculoides_PRJNA270931 100 Opisthokonta-Metazoa_Annelida_Polychaeta_Capitellida_Capitellidae_Capitella_teleta_GCA_000328365.1 Opisthokonta-Metazoa_Brachiopoda_Lingulata_Lingulida_Lingulidae_Lingula_anatina_GCA_001039355.1100 100 Opisthokonta-Metazoa_Chordata_Aves_Galliformes_Phasianidae_Gallus_gallus_N/A 99 Opisthokonta-Metazoa_Chordata_Aves_Galliformes_Phasianidae_Gallus_gallus_Gallus_gallus-5.0 100 Opisthokonta-Metazoa_Chordata_Aves_Anseriformes_Anatidae_Anas_platyrhynchos_BGI_duck_1.0 100 Opisthokonta-Metazoa_Chordata_N/A_Testudines_Trionychidae_Pelodiscus_sinensis_PelSin_1.0 100 100 Opisthokonta-Metazoa_Chordata_N/A_Squamata_Iguanidae_Anolis_carolinensis_AnoCar2.0 100 100 Opisthokonta-Metazoa_Chordata_Mammalia_Rodentia_Muridae_Rattus_norvegicus_N/A Opisthokonta-Metazoa_Chordata_Mammalia_Rodentia_Muridae_Mus_musculus_N/A 100 Opisthokonta-Metazoa_Chordata_Mammalia_Primates_Hominidae_Homo_sapiens_N/A 100 Opisthokonta-Metazoa_Chordata_Amphibia_Anura_Pipidae_Xenopus_tropicalis_JGI_4.2 Opisthokonta-Metazoa_Chordata_N/A_Coelacanthiformes_Coelacanthidae_Latimeria_chalumnae_LatCha1 70 100 100 Opisthokonta-Metazoa_Chordata_Actinopteri_Tetraodontiformes_Tetraodontidae_Takifugu_rubripes_FUGU4 100 Opisthokonta-Metazoa_Chordata_Actinopteri_Cypriniformes_Cyprinidae_Danio_rerio_N/A Opisthokonta-Metazoa_Chordata_N/A_Petromyzontiformes_Petromyzontidae_Petromyzon_marinus_Pmarinus_7.0 100 100 Opisthokonta-Metazoa_Chordata_Ascidiacea_Enterogona_Cionidae_Ciona_intestinalis_N/A 100 Opisthokonta-Metazoa_Chordata_Ascidiacea_Enterogona_Cionidae_Ciona_intestinalis_KH 100 Opisthokonta-Metazoa_Chordata_N/A_N/A_Branchiostomidae_Branchiostoma_floridae_N/A Opisthokonta-Metazoa_Echinodermata_Echinoidea_Echinoida_Strongylocentrotidae_Strongylocentrotus_purpuratus_GCA_000002235.2 100 100 Opisthokonta-Metazoa_Cnidaria_Anthozoa_Actiniaria_Edwardsiidae_Nematostella_vectensis_N/A 70 Opisthokonta-Metazoa_Placozoa_N/A_N/A_N/A_Trichoplax_adhaerens_N/A Opisthokonta-Metazoa_Placozoa_N/A_N/A_N/A_Trichoplax_adhaerens_ASM15027v1 100 Opisthokonta-Metazoa_Porifera_Demospongiae_Haplosclerida_Niphatidae_Amphimedon_queenslandica_Aqu1 100 Opisthokonta-Metazoa_Ctenophora_Tentaculata_Lobata_Bolinopsidae_Mnemiopsis_leidyi_GCA_000226015.1 100 Opisthokonta-Choanoflagellatea_N/A_N/A_Choanoflagellida_Salpingoecidae_Salpingoeca_rosetta_Proterospongia_sp_ATCC50818 100 Opisthokonta-Choanoflagellatea_N/A_N/A_Choanoflagellida_Salpingoecidae_Salpingoeca_sp_N/A Opisthokonta-Choanoflagellatea_N/A_N/A_Choanoflagellida_Codonosigidae_Monosiga_brevicollis_N/A 98 100 Opisthokonta-Undef_N/A_N/A_N/A_N/A_N/A_N/A_10tr 100 Opisthokonta-Ichthyosporea_N/A_Ichthyosporea_Ichthyophonida_N/A_Ichthyophonus_hoferi_SRR2134855 100 Opisthokonta-Ichthyosporea_N/A_Ichthyosporea_Ichthyophonida_N/A_Ichthyophonus_hoferi_SRR1618711 100 Opisthokonta-Ichthyosporea_N/A_Ichthyosporea_Ichthyophonida_Amoebidiaceae_Amoebidium_parasiticum_SRR545192 100 100 Opisthokonta-Ichthyosporea_N/A_Ichthyosporea_Ichthyophonida_N/A_Sphaeroforma_arctica_N/A Opisthokonta-Ichthyosporea_N/A_Ichthyosporea_Ichthyophonida_N/A_Sphaeroforma_arctica_Spha_arctica_JP610_V1 100 100 Opisthokonta-Ichthyosporea_N/A_Ichthyosporea_N/A_N/A_Pirum_gemmata_SRR1029663 Opisthokonta-Ichthyosporea_N/A_Ichthyosporea_N/A_N/A_Abeoforma_whisleri_SRR1029669 99 100 Opisthokonta-Ichthyosporea_N/A_Ichthyosporea_Dermocystida_N/A_Sphaerothecum_destruens_SRR1618479 100 Opisthokonta-Corallosporea_N/A_N/A_N/A_N/A_Corallochytrium_limacisporum_SRR1618557 Opisthokonta-Corallosporea_N/A_N/A_N/A_N/A_Corallochytrium_limacisporum_SRR1618598 100 Opisthokonta-Undef_N/A_N/A_N/A_N/A_N/A_N/A_Colp12 100 Opisthokonta-Filasterea_N/A_Ichthyosporea_N/A_N/A_Capsaspora_owczarzaki_N/A Opisthokonta-Filasterea_N/A_Ichthyosporea_N/A_N/A_Capsaspora_owczarzaki_C_owczarzaki_V2100 100 Opisthokonta-Fungi_Ascomycota_Saccharomycetes_Saccharomycetales_Debaryomycetaceae_Debaryomyces_hansenii_N/A 100 Opisthokonta-Fungi_Ascomycota_Saccharomycetes_Saccharomycetales_Debaryomycetaceae_Debaryomyces_hansenii_J26 Opisthokonta-Fungi_Ascomycota_Saccharomycetes_Saccharomycetales_Saccharomycetaceae_Saccharomyces_cerevisiae_Sc_YJM1078_v1 100 100 Opisthokonta-Fungi_Ascomycota_Saccharomycetes_Saccharomycetales_Dipodascaceae_Yarrowia_lipolytica_N/A 100 100 Opisthokonta-Fungi_Ascomycota_Sordariomycetes_Sordariales_Sordariaceae_Neurospora_crassa_N/A 100 Opisthokonta-Fungi_Ascomycota_Sordariomycetes_Hypocreales_Nectriaceae_Fusarium_graminearum_N/A 100 Opisthokonta-Fungi_Ascomycota_Eurotiomycetes_Eurotiales_Aspergillaceae_Aspergillus_oryzae_AspOry3042 100 Opisthokonta-Fungi_Ascomycota_Eurotiomycetes_Eurotiales_Aspergillaceae_Aspergillus_niger_N/A 100 Opisthokonta-Fungi_Ascomycota_Schizosaccharomycetes_Schizosaccharomycetales_Schizosaccharomycetaceae_Schizosaccharomyces_pombe_N/A 100 Opisthokonta-Fungi_Ascomycota_Schizosaccharomycetes_Schizosaccharomycetales_Schizosaccharomycetaceae_Schizosaccharomyces_pombe_ASM294v2 100 Opisthokonta-Fungi_Basidiomycota_Agaricomycetes_Agaricales_Tricholomataceae_Laccaria_bicolor_N/A 99 100 Opisthokonta-Fungi_Basidiomycota_Agaricomycetes_Agaricales_Psathyrellaceae_Coprinopsis_cinerea_N/A Opisthokonta-Fungi_Basidiomycota_Tremellomycetes_Tremellales_Cryptococcaceae_Cryptococcus_neoformans_N/A Opisthokonta-Fungi_Basidiomycota_Ustilaginomycetes_Ustilaginales_Ustilaginaceae_Ustilago_maydis_N/A 100 100 100 Opisthokonta-Fungi_Mucoromycota_N/A_Mucorales_Rhizopodaceae_Rhizopus_delemar_RO3 100 Opisthokonta-Fungi_Mucoromycota_N/A_Mucorales_Phycomycetaceae_Phycomyces_blakesleeanus_N/A 100 Opisthokonta-Fungi_Mucoromycota_Glomeromycetes_Glomerales_Glomeraceae_Rhizophagus_irregularis_Rir 100 Opisthokonta-Fungi_Zoopagomycota_Entomophthoromycetes_Entomophthorales_Ancylistaceae_Conidiobolus_coronatus_Conidiobolus_coronatus_NRRL28638 100 Opisthokonta-Fungi_Chytridiomycota_Chytridiomycetes_Spizellomycetales_Spizellomycetaceae_Spizellomyces_punctatus_S_punctatus_V1 100 84 Opisthokonta-Fungi_Chytridiomycota_Chytridiomycetes_Rhizophydiales_N/A_Batrachochytrium_dendrobatidis_N/A Opisthokonta-Fungi_Chytridiomycota_Monoblepharidomycetes_Monoblepharidales_Gonapodyaceae_Gonapodya_prolifera_Ganpr1 100 100 Opisthokonta-Fungi_Blastocladiomycota_Blastocladiomycetes_Blastocladiales_Blastocladiaceae_Allomyces_macrogynus_A_macrogynus_V3 100 Opisthokonta-Fungi_Cryptomycota_N/A_N/A_N/A_Rozella_allomycis_N/A Opisthokonta-Fungi_Cryptomycota_N/A_N/A_N/A_Rozella_allomycis_Rozella_k41_t100 100 Opisthokonta-Discicristoidea_N/A_N/A_N/A_Nucleariidae_Nuclearia_sp_SRR1617645 Opisthokonta-Discicristoidea_N/A_N/A_N/A_N/A_Fonticula_alba_Font_alba_ATCC_38817_V2 100 Breviatea_N/A_N/A_N/A_N/A_Pygsuia_biforma_N/A 100 Breviatea_N/A_N/A_N/A_N/A_Breviata_anathema_N/A 100 Apusomonadida_N/A_N/A_N/A_Apusomonadidae_Thecamonas_trahens_N/A 78 100 Apusomonadida_N/A_N/A_N/A_Apusomonadidae_Amastigomonas_sp_N/A 100 Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N/A_Dictyostelium_purpureum_N/A Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N/A_Dictyostelium_discoideum_N/A 100 Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N/A_Dictyostelium_lacteum_ASM160615v1 100 100 Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N/A_Dictyostelium_fasciculatum_DFas_2.0 94 Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N/A_Polysphondylium_pallidum_N/A 97 Amoebozoa_Evosea_Eumycetozoa_Physariida_Physaraceae_Physarum_polycephalum_N/A Amoebozoa_Evosea_Archamoebae_N/A_Mastigamoebidae_Mastigamoeba_balamuthi_N/A 94 Amoebozoa_Evosea_Variosea_N/A_Echinamoebidae_Filamoeba_nolandi_NC-AS-23-1 100 Amoebozoa_Tubulinea_Elardia_Arcellinida_Difflugiidae_Sexangularia_sp_ATCC50979 94 Amoebozoa_Tubulinea_N/A_N/A_N/A_misidentifiedPessonella_sp_PRA-29 100 Amoebozoa_Tubulinea_Echinamoebidia_N/A_Hartmannellidae_Vermamoeba_vermiformis_N/A 100 Amoebozoa_Tubulinea_Corycidia_N/A_N/A_Trichosphaerium_sp_Am-I-7wt 100 100 Amoebozoa_Discosea_Flabellinia_N/A_Paramoebidae_Paramoeba_aestuarina_SoJaBioB1-5_56_2 100 Amoebozoa_Discosea_Flabellinia_N/A_Paramoebidae_Paramoeba_atlantica_CCAP1560_9 Amoebozoa_Discosea_Flabellinia_N/A_N/A_Cunea_sp_BSH-02190019_may 100 100 Amoebozoa_Discosea_Flabellinia_N/A_Vexilliferidae_Vexillifera_sp_DIVA3564_2 95 Amoebozoa_Discosea_Flabellinia_N/A_Vannellidae_Vannella_sp_DIVA3517_6_12 94 Amoebozoa_Discosea_Flabellinia_N/A_Vannellidae_Vannella_robusta_DIVA3518_3_11_1_6 100 Amoebozoa_Discosea_Flabellinia_N/A_N/A_Stygamoeba_regulata_BSH-02190019_sty 100 Amoebozoa_Discosea_Centramoebia_Longamoebia_N/A_Acanthamoeba_castellanii_N/A Amoebozoa_Discosea_Centramoebia_Longamoebia_N/A_Acanthamoeba_castellanii_Acastellanii_strNEFF_v1 100 Amoebozoa_Discosea_N/A_N/A_N/A_Stereomyxa_ramosa_Chinc5 100 Diphyllatia_N/A_N/A_N/A_Collodictyonidae_Collodictyon_sp_N/A Diphyllatia_N/A_N/A_N/A_Collodictyonidae_Diphylleia_rotans_N/A 100 Rigifilida_N/A_N/A_Rigifilida_N/A_Rigifila_ramosa_N/A 100 Excavata-Undef_N/A_N/A_N/A_Malawimonadidae_Malawimonas_jakobiformis_N/A Excavata-Undef_N/A_N/A_N/A_Malawimonadidae_Malawimonas_californiana_N/A 100 Excavata-Undef_N/A_N/A_N/A_Malawimonadidae_Gefionella_okellyi_N/A 100 Apusozoa_Apusozoa_N/A_N/A_N/A_Nutomonas_longa_SRR1617398 Ancyromonadida_N/A_N/A_N/A_N/A_Nutomonas_longa_N/A Ancyromonadida_N/A_N/A_Ancyromonadida_Ancyromonadidae_Ancyromonas_sigmoides_N/A Ancyromonadida_N/A_N/A_N/A_Planomonadidae_Fabomonas_tropica_N/A

0.3

Supplementary Figure 3: Maximum likelihood tree of 794 eukaryotic species. The tree is based on the concatenated alignment of 317 marker genes (filtered with Divvier) and was reconstructed using the site- homogeneous model LG+F+G. Support values correspond to 1000 ultrafast bootstrap replicates.

5 100

80

60

40 UFboot support Picozoa+Rhodelphis+Rhodophyta Rhodelphis+Rhodophyta 20 Archaeplastida Archaeplastida+Cryptista Amorphea TSAR 0 SAR

5000 10000 15000 20000 25000 30000 35000 40000 45000 50000 55000 Number of removed sites

Supplementary Figure 4: Support for several groupings as estimated in different trees with increasing number of fast-evolving sites removed. Initial alignment was the 67-dataset (filtered with BMGE). All trees were reconstructed using the site-heterogeneous model LG+C60+F+G, support values correspond to 1000 ultrafast bootstrap replicates

100 96 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Pyramimonadales_N/A_Pyramimonas_parkeae_CCMP726 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Prasinococcales_N/A_Prasinoderma_singulare_RCC927 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Volvocaceae_Volvox_carteri_N/A 100 Archaeplastida-Viridiplantae_Streptophyta_Bryopsida_Funariales_Funariaceae_Physcomitrella_patens_N/A 99 Archaeplastida-Viridiplantae_Streptophyta_N/A_Brassicales_Brassicaceae_Arabidopsis_thaliana_TAIR10 99 100 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_Gloeochaetales_Gloeochaetaceae_Gloeochaete_wittrockiana_SAG46.84 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_Cyanophoraceae_Cyanophora_paradoxa_N/A Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_N/A_Cyanoptyche_gloeocystis_SAG4.97 87 100 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Geminigera_merged_sp_cryophila Cryptista_Cryptophyta_Cryptophyta_N/A_N/A_Cryptophyceae_sp_merged_CCMP2293_N/A 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Chroomonadaceae_Chroomonas_mesostigmatica_CCMP1168 100 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_pacifica_merged_CCMP1869_N/A 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_merged_sp_avonlea Cryptista_Katablepharida_Katablepharidophyta_N/A_N/A_Roombia_truncata_N/A Cryptista_Palpitia_N/A_N/A_N/A__Palpitomonas_bilix_merged_NIES-2562_N/A 99 97 100 Archaeplastida-Rhodophyta_Rhodophyta_Compsopogonophyceae_Compsopogonales_Compsopogonaceae_Compsopogon_caeruleus_SAG36.94 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Porphyridium_purpureum_N/A 100 Archaeplastida-Rhodophyta_Rhodophyta_Stylonematophyceae_Stylonematales_Stylonemataceae_Rhodosorus_marinus_merged_UTEXLB2760_CCMP769 100 100 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gigartinales_Gigartinaceae_Chondrus_crispus_N/A Archaeplastida-Rhodophyta_Rhodophyta_Bangiophyceae_Bangiales_Bangiaceae_merged_Porphyra_Pyropia 69 93 Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Galdieria_sulphuraria_N/A 30 Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Cyanidioschyzon_merolae_N/A 100 100 Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_marinus_merged_Colp29_N/A Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_limneticus_N/A 100 100 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A__merged_COSAG02_COSAG03_COSAG04_COSAG06 Picozoa_Picozoa_N/A_N/A_N/A_merged_Picobiliphyte_sp_MS584-11_COSAG05_COSAG01_SAG25 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_merged_SAG22_SAG31_SAG11 Hemimastigophora_N/A_N/A_N/A_Spironemidae_Hemimastix_kukwesjijk_N/A 100 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_merged_C15_C1 100 Alveolata_Dinophyta_Dinophyceae_Oxyrrhinales_Oxyrrhinaceae_Oxyrrhis_marina_merged_CCMP1795_LB1974_js006_N/A 100 99 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Sarcocystidae_Hammondia_hammondi_HHA1_v02 Alveolata_Chrompodelida_N/A_N/A_N/A_Vitrella_brassicaformis_merged_CCMP3155_Vbrassicaformis 100 100 93 Alveolata_Ciliophora_Spirotrichea_Sporadotrichida_Oxytrichidae_Oxytricha_trifallax_oxytricha_asm_v1.1 Alveolata_Ciliophora_Oligohymenophorea_Hymenostomatida_Tetrahymenidae_Tetrahymena_thermophila_N/A Alveolata_Colponemidia_N/A_N/A_N/A_N/A_N/A_merged_Colp15_Colp10 100 100 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Pelagomonadales_N/A_Pelagomonas_calceolata_merged_RCC969_CCMP1756 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_rotula_CCMP3096 100 100 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Paraphysomonadaceae_Paraphysomonas_bandaiensis_js007 Stramenopila-Oomycota_N/A_Oomycetes_Saprolegniales_Saprolegniaceae_Saprolegnia_diclina_Sap_diclina_VS20_V1 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Aplanochytrium_merged_kerguelense_sp 100 75 100 Rhizaria_N/A_N/A_N/A_N/A_N/A_N/A_D1 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Bigelowiella_natans_N/A Rhizaria_Phytorhiza_N/A_N/A_Plasmodiophoridae_Plasmodiophora_brassicae_pbe3.h15 100 Telonemia_N/A_N/A_Telonemida_N/A_Telonema_subtile_merged_Tel-1_N/A 38 Telonemia_N/A_N/A_Telonemida_N/A_N/A_N/A_P-2 100 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Prymnesium_parvum_merged_Texoma1_N/A Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_merged_PLYM219_374_379_CCMP370_N/A 97 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_merged_Pavlovales_N/A 94 100 Haptista_Centrohelida_N/A_N/A_Raphidiophryidae_Raphidiophrys_heterophryoidea_N/A Haptista_Centrohelida_N/A_N/A_Acanthocystidae_Choanocystis_sp_N/A Haptista-sister_N/A_N/A_N/A_N/A_Ancoracysta_twista_TD 100 Opisthokonta-Fungi_Chytridiomycota_Chytridiomycetes_Spizellomycetales_Spizellomycetaceae_Spizellomyces_punctatus_S_punctatus_V1 100 Opisthokonta-Discicristoidea_N/A_N/A_N/A_Nucleariidae_Nuclearia_sp_SRR1617645 94 100 Opisthokonta-Filasterea_N/A_Ichthyosporea_N/A_N/A_Capsaspora_owczarzaki_merged_C_N/A 82 Opisthokonta-Metazoa_Chordata_Mammalia_Rodentia_Muridae_Mus_musculus_N/A Apusomonadida_N/A_N/A_N/A_Apusomonadidae_Thecamonas_trahens_N/A 100 Breviatea_N/A_N/A_N/A_N/A_Pygsuia_biforma_N/A 93 100 Amoebozoa_Tubulinea_N/A_N/A_N/A_misidentifiedPessonella_sp_PRA-29 97 Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N/A_Dictyostelium_lacteum_ASM160615v1 Amoebozoa_Discosea_N/A_N/A_N/A_Stereomyxa_ramosa_Chinc5 100 Ancyromonadida_N/A_N/A_N/A_N/A_Nutomonas_longa_merged_SRR1617398_N/A 93 Ancyromonadida_N/A_N/A_N/A_Planomonadidae_Fabomonas_tropica_N/A 100 100 Excavata-Discoba_Percolozoa_Heterolobosea_N/A_N/A_Percolomonas_cosmopolitus_WS Excavata-Discoba_Percolozoa_Heterolobosea_Schizopyrenida_Vahlkampfiidae_Naegleria_gruberi_N/A 78 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Bodonidae_Bodo_saltans_N/A 100 Excavata-Metamonada_Metamonada_N/A_Oxymonadida_Polymastigidae_Monocercomonoides_sp_PA203 Excavata-Metamonada_Metamonada_N/A_N/A_N/A_Paratrimastix_pyriformis_merged_js010_N/A

0.2

Supplementary Figure 5: Maximum likelihood tree of 67 eukaryotic species showing the position of Pi- cozoa. The tree is based on the concatenated alignment of 317 marker genes, filtered with BMGE and trimmed of the 25% most heterogenous sites according to the chi-square statistic. The tree was reconstructed using the site-heterogeneous model LG+C60+F+G, support values correspond to 1000 ultrafast bootstrap replicates.

6 Supplementary Figure 6: Multi-species coalescent species tree reconstructed with ASTRAL-III. Individ- ual single gene trees were inferred for all 317 untrimmed alignments from the 67-taxa dataset, using automatic model selection and 1000 ultrafast bootstraps. Support values correspond to multi-locus bootstraps and pos- terior probabilities, respectively.

7 100 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Geminigera_merged_sp_cryophila Cryptista_Cryptophyta_Cryptophyta_N/A_N/A_Cryptophyceae_sp_merged_CCMP2293_N/A 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Chroomonadaceae_Chroomonas_mesostigmatica_CCMP1168 100 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_pacifica_merged_CCMP1869_N/A 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_merged_sp_avonlea 42 Cryptista_Katablepharida_Katablepharidophyta_N/A_N/A_Roombia_truncata_N/A Cryptista_Palpitia_N/A_N/A_N/A__Palpitomonas_bilix_merged_NIES-2562_N/A Haptista-sister_N/A_N/A_N/A_N/A_Ancoracysta_twista_TD 96 43 96 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Pyramimonadales_N/A_Pyramimonas_parkeae_CCMP726 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Prasinococcales_N/A_Prasinoderma_singulare_RCC927 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Volvocaceae_Volvox_carteri_N/A 100 Archaeplastida-Viridiplantae_Streptophyta_Bryopsida_Funariales_Funariaceae_Physcomitrella_patens_N/A 97 Archaeplastida-Viridiplantae_Streptophyta_N/A_Brassicales_Brassicaceae_Arabidopsis_thaliana_TAIR10 94 100 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_Gloeochaetales_Gloeochaetaceae_Gloeochaete_wittrockiana_SAG46.84 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_Cyanophoraceae_Cyanophora_paradoxa_N/A Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_N/A_Cyanoptyche_gloeocystis_SAG4.97 47 99 99 Archaeplastida-Rhodophyta_Rhodophyta_Compsopogonophyceae_Compsopogonales_Compsopogonaceae_Compsopogon_caeruleus_SAG36.94 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Porphyridium_purpureum_N/A 100 Archaeplastida-Rhodophyta_Rhodophyta_Stylonematophyceae_Stylonematales_Stylonemataceae_Rhodosorus_marinus_merged_UTEXLB2760_CCMP769 100 100 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gigartinales_Gigartinaceae_Chondrus_crispus_N/A Archaeplastida-Rhodophyta_Rhodophyta_Bangiophyceae_Bangiales_Bangiaceae_merged_Porphyra_Pyropia 99 94 Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Galdieria_sulphuraria_N/A Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Cyanidioschyzon_merolae_N/A 100 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A__merged_COSAG02_COSAG03_COSAG04_COSAG06 100 100 Picozoa_Picozoa_N/A_N/A_N/A_merged_Picobiliphyte_sp_MS584-11_COSAG05_COSAG01_SAG25 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_merged_SAG22_SAG31_SAG11 100 Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_marinus_merged_Colp29_N/A Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_limneticus_N/A 100 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_merged_C15_C1 100 Alveolata_Dinophyta_Dinophyceae_Oxyrrhinales_Oxyrrhinaceae_Oxyrrhis_marina_merged_CCMP1795_LB1974_js006_N/A 100 97 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Sarcocystidae_Hammondia_hammondi_HHA1_v02 94 Alveolata_Chrompodelida_N/A_N/A_N/A_Vitrella_brassicaformis_merged_CCMP3155_Vbrassicaformis 100 100 Alveolata_Ciliophora_Spirotrichea_Sporadotrichida_Oxytrichidae_Oxytricha_trifallax_oxytricha_asm_v1.1 Alveolata_Ciliophora_Oligohymenophorea_Hymenostomatida_Tetrahymenidae_Tetrahymena_thermophila_N/A Alveolata_Colponemidia_N/A_N/A_N/A_N/A_N/A_merged_Colp15_Colp10 96 100 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Pelagomonadales_N/A_Pelagomonas_calceolata_merged_RCC969_CCMP1756 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_rotula_CCMP3096 100 100 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Paraphysomonadaceae_Paraphysomonas_bandaiensis_js007 Stramenopila-Oomycota_N/A_Oomycetes_Saprolegniales_Saprolegniaceae_Saprolegnia_diclina_Sap_diclina_VS20_V1 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Aplanochytrium_merged_kerguelense_sp 100 100 Rhizaria_N/A_N/A_N/A_N/A_N/A_N/A_D1 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Bigelowiella_natans_N/A 69 Rhizaria_Phytorhiza_N/A_N/A_Plasmodiophoridae_Plasmodiophora_brassicae_pbe3.h15 100 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Prymnesium_parvum_merged_Texoma1_N/A Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_merged_PLYM219_374_379_CCMP370_N/A 88 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_merged_Pavlovales_N/A 35 100 68 Haptista_Centrohelida_N/A_N/A_Raphidiophryidae_Raphidiophrys_heterophryoidea_N/A Haptista_Centrohelida_N/A_N/A_Acanthocystidae_Choanocystis_sp_N/A 100 Telonemia_N/A_N/A_Telonemida_N/A_Telonema_subtile_merged_Tel-1_N/A Telonemia_N/A_N/A_Telonemida_N/A_N/A_N/A_P-2 Hemimastigophora_N/A_N/A_N/A_Spironemidae_Hemimastix_kukwesjijk_N/A 100 Opisthokonta-Fungi_Chytridiomycota_Chytridiomycetes_Spizellomycetales_Spizellomycetaceae_Spizellomyces_punctatus_S_punctatus_V1 100 Opisthokonta-Discicristoidea_N/A_N/A_N/A_Nucleariidae_Nuclearia_sp_SRR1617645 100 93 Opisthokonta-Filasterea_N/A_Ichthyosporea_N/A_N/A_Capsaspora_owczarzaki_merged_C_N/A Opisthokonta-Metazoa_Chordata_Mammalia_Rodentia_Muridae_Mus_musculus_N/A 75 100 Apusomonadida_N/A_N/A_N/A_Apusomonadidae_Thecamonas_trahens_N/A Breviatea_N/A_N/A_N/A_N/A_Pygsuia_biforma_N/A 92 100 Amoebozoa_Tubulinea_N/A_N/A_N/A_misidentifiedPessonella_sp_PRA-29 76 Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N/A_Dictyostelium_lacteum_ASM160615v1 Amoebozoa_Discosea_N/A_N/A_N/A_Stereomyxa_ramosa_Chinc5 95 100 Excavata-Metamonada_Metamonada_N/A_Oxymonadida_Polymastigidae_Monocercomonoides_sp_PA203 Excavata-Metamonada_Metamonada_N/A_N/A_N/A_Paratrimastix_pyriformis_merged_js010_N/A 94 100 Ancyromonadida_N/A_N/A_N/A_N/A_Nutomonas_longa_merged_SRR1617398_N/A Ancyromonadida_N/A_N/A_N/A_Planomonadidae_Fabomonas_tropica_N/A 100 100 Excavata-Discoba_Percolozoa_Heterolobosea_N/A_N/A_Percolomonas_cosmopolitus_WS Excavata-Discoba_Percolozoa_Heterolobosea_Schizopyrenida_Vahlkampfiidae_Naegleria_gruberi_N/A Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Bodonidae_Bodo_saltans_N/A

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Supplementary Figure 7: Maximum likelihood tree of 67 eukaryotic species showing the position of Pi- cozoa. The tree is based on the concatenated alignment of 317 marker genes, filtered with BMGE and trimmed of the 50% most heterogenous sites according to the chi-square statistic. The tree was reconstructed using the site-heterogeneous model LG+C60+F+G, support values correspond to 1000 ultrafast bootstrap replicates.

8 89 70 Archaeplastida-Rhodophyta_Rhodophyta_Compsopogonophyceae_Compsopogonales_Compsopogonaceae_Compsopogon_caeruleus_SAG36.94 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Porphyridium_purpureum_N/A 100 Archaeplastida-Rhodophyta_Rhodophyta_Stylonematophyceae_Stylonematales_Stylonemataceae_Rhodosorus_marinus_merged_UTEXLB2760_CCMP769 100 100 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gigartinales_Gigartinaceae_Chondrus_crispus_N/A Archaeplastida-Rhodophyta_Rhodophyta_Bangiophyceae_Bangiales_Bangiaceae_merged_Porphyra_Pyropia 100 50 Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Galdieria_sulphuraria_N/A Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Cyanidioschyzon_merolae_N/A 100 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A__merged_COSAG02_COSAG03_COSAG04_COSAG06 100 100 Picozoa_Picozoa_N/A_N/A_N/A_merged_Picobiliphyte_sp_MS584-11_COSAG05_COSAG01_SAG25 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_merged_SAG22_SAG31_SAG11 100 Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_marinus_merged_Colp29_N/A Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_limneticus_N/A 30 95 100 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Pyramimonadales_N/A_Pyramimonas_parkeae_CCMP726 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Prasinococcales_N/A_Prasinoderma_singulare_RCC927 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Volvocaceae_Volvox_carteri_N/A 100 Archaeplastida-Viridiplantae_Streptophyta_Bryopsida_Funariales_Funariaceae_Physcomitrella_patens_N/A 98 Archaeplastida-Viridiplantae_Streptophyta_N/A_Brassicales_Brassicaceae_Arabidopsis_thaliana_TAIR10 60 100 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_N/A_Cyanoptyche_gloeocystis_SAG4.97 100 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_Gloeochaetales_Gloeochaetaceae_Gloeochaete_wittrockiana_SAG46.84 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_Cyanophoraceae_Cyanophora_paradoxa_N/A 100 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Geminigera_merged_sp_cryophila Cryptista_Cryptophyta_Cryptophyta_N/A_N/A_Cryptophyceae_sp_merged_CCMP2293_N/A 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Chroomonadaceae_Chroomonas_mesostigmatica_CCMP1168 100 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_pacifica_merged_CCMP1869_N/A 51 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_merged_sp_avonlea Cryptista_Katablepharida_Katablepharidophyta_N/A_N/A_Roombia_truncata_N/A Cryptista_Palpitia_N/A_N/A_N/A__Palpitomonas_bilix_merged_NIES-2562_N/A 100 100 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Prymnesium_parvum_merged_Texoma1_N/A Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_merged_PLYM219_374_379_CCMP370_N/A 95 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_merged_Pavlovales_N/A 67 100 Haptista_Centrohelida_N/A_N/A_Raphidiophryidae_Raphidiophrys_heterophryoidea_N/A Haptista_Centrohelida_N/A_N/A_Acanthocystidae_Choanocystis_sp_N/A Haptista-sister_N/A_N/A_N/A_N/A_Ancoracysta_twista_TD 100 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_merged_C15_C1 100 Alveolata_Dinophyta_Dinophyceae_Oxyrrhinales_Oxyrrhinaceae_Oxyrrhis_marina_merged_CCMP1795_LB1974_js006_N/A 44 100 94 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Sarcocystidae_Hammondia_hammondi_HHA1_v02 Alveolata_Chrompodelida_N/A_N/A_N/A_Vitrella_brassicaformis_merged_CCMP3155_Vbrassicaformis 100 100 Alveolata_Ciliophora_Spirotrichea_Sporadotrichida_Oxytrichidae_Oxytricha_trifallax_oxytricha_asm_v1.1 Alveolata_Ciliophora_Oligohymenophorea_Hymenostomatida_Tetrahymenidae_Tetrahymena_thermophila_N/A Alveolata_Colponemidia_N/A_N/A_N/A_N/A_N/A_merged_Colp15_Colp10 100 95 100 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Pelagomonadales_N/A_Pelagomonas_calceolata_merged_RCC969_CCMP1756 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_rotula_CCMP3096 98 100 100 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Paraphysomonadaceae_Paraphysomonas_bandaiensis_js007 Stramenopila-Oomycota_N/A_Oomycetes_Saprolegniales_Saprolegniaceae_Saprolegnia_diclina_Sap_diclina_VS20_V1 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Aplanochytrium_merged_kerguelense_sp 100 74 100 Rhizaria_N/A_N/A_N/A_N/A_N/A_N/A_D1 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Bigelowiella_natans_N/A Rhizaria_Phytorhiza_N/A_N/A_Plasmodiophoridae_Plasmodiophora_brassicae_pbe3.h15 100 Telonemia_N/A_N/A_Telonemida_N/A_Telonema_subtile_merged_Tel-1_N/A Telonemia_N/A_N/A_Telonemida_N/A_N/A_N/A_P-2 91 Hemimastigophora_N/A_N/A_N/A_Spironemidae_Hemimastix_kukwesjijk_N/A 100 Opisthokonta-Fungi_Chytridiomycota_Chytridiomycetes_Spizellomycetales_Spizellomycetaceae_Spizellomyces_punctatus_S_punctatus_V1 100 Opisthokonta-Discicristoidea_N/A_N/A_N/A_Nucleariidae_Nuclearia_sp_SRR1617645 100 99 Opisthokonta-Filasterea_N/A_Ichthyosporea_N/A_N/A_Capsaspora_owczarzaki_merged_C_N/A Opisthokonta-Metazoa_Chordata_Mammalia_Rodentia_Muridae_Mus_musculus_N/A 88 100 Apusomonadida_N/A_N/A_N/A_Apusomonadidae_Thecamonas_trahens_N/A Breviatea_N/A_N/A_N/A_N/A_Pygsuia_biforma_N/A 85 100 Amoebozoa_Tubulinea_N/A_N/A_N/A_misidentifiedPessonella_sp_PRA-29 97 Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N/A_Dictyostelium_lacteum_ASM160615v1 Amoebozoa_Discosea_N/A_N/A_N/A_Stereomyxa_ramosa_Chinc5 100 Ancyromonadida_N/A_N/A_N/A_N/A_Nutomonas_longa_merged_SRR1617398_N/A Ancyromonadida_N/A_N/A_N/A_Planomonadidae_Fabomonas_tropica_N/A 100 100 Excavata-Discoba_Percolozoa_Heterolobosea_N/A_N/A_Percolomonas_cosmopolitus_WS Excavata-Discoba_Percolozoa_Heterolobosea_Schizopyrenida_Vahlkampfiidae_Naegleria_gruberi_N/A 91 Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Bodonidae_Bodo_saltans_N/A 100 Excavata-Metamonada_Metamonada_N/A_Oxymonadida_Polymastigidae_Monocercomonoides_sp_PA203 Excavata-Metamonada_Metamonada_N/A_N/A_N/A_Paratrimastix_pyriformis_merged_js010_N/A

0.2

Supplementary Figure 8: Maximum likelihood tree of 67 eukaryotic species showing the position of Picozoa. The tree is based on the concatenated alignment of 224 marker genes with at least two monophyletic Picozoa sequences (filtered with BMGE). The tree was reconstructed using the site-heterogeneous model LG+C60+F+G, support values correspond to 1000 ultrafast bootstrap replicates.

9 nad 6

orf 106

rpl 16 rps 4 orf 113 F cox 3 cox 2 nad 2 nad 6

rps 13 P G cox 1 D orf 112

A. nad1

N rps 8 rps 19 H W nad 4L I T E R orf 101 rps2 rns D nad 5 rrn5 cox 2 rps 8 M rps12 rps 3 R C cob K nad 4 rps1 Y C nad4Lnad4L nad 3 rps19 L rpl14 rpl 5 rps7 S rps 3 rps4 rpl 6 rps 8 cob cox2 nad 5 5nad cox 1 Y D atp9 L Q nad6 F rpl 16 rps12 E E Y N orf 162 V M D nad 1 K rpl 5 V Q nad 3 A rnl A S Picozoa sp. MS584-11 rpl 14 M rps 14 M Picozoa 8/12 atp 6 Picozoa 43 nad 5 rps14 I S atp 9 L rns A 49008bp Q atp 6 T rpl6 54,420 bp orf115 ~56,000 bp G L rnl rps 14 L nad3 orf 338 V nad 4 orf 129 nad 4L rpl 5 A nad1 rps1 cob

M R W rps3 W C rps 13 rpl 6 nad 2 rps 2 orf 236 cox 1

cox 3 rps 19 orf 146 S rpl 14 atp 8 L T nad 2 K rpl 16 rps 7 rns H H N atp 8 rps 4

nad4 F cox 3 M I rnl rps 2 rps 7 P orf 108 rnl B orf 110 rps1 S atp 9 S rps 13 atp 8 atp 6 rnl

rps 12

orf 134 rps 2

rns rps 2 cox 2 P cox 3 nad 4L orf 100

S rpl 14 C S cox 3 cob rpl 14rpl 14 R -F R cox 1

rps 3 orf 228 A rps 13 nad 1 rps 19 nad 5 orf 165 orf 106 nad 1 rnl B T rps 14 N I rnl 1 G nad 6 rnl B atp 8 nad 3 rps 4 rnl

rnl B? nad 2

W L Picozoa 22 orf 116 rps 8 Picozoa 11 H atp 9 orf 148 R nad 4 61,565 bp rpl 5 nad 6 >48,000 bp rpl 6 rps 12 orf 105_1 rps 4 orf 561 orf 287 V rps 12 Q K F V Y L orf 173 K E orf 146 L Q D atp 6 Y M D rps 7 orf 316 rpl 5 orf 152 rps 8 orf 99 orf 192 cox 1 cox 2P rps 7 nad 5 rps 19 atp 9 rps 13 M

R A

M

T atp 6 nad 2 rps 1 M rps 14 I

orf 786 G rnl N orf 185

cob atp 8

nad 4

Mitoribosomal RNA ETC subunits B. Protein Subunits genes cox1 cox2 cox3 atp6 atp8 atp9 cob rns rnl s1 s2 s3 s4 s7 s8 s12 s13 s14 s19 L5 L6 L14 L16 nad1 nad2 nad3 nad4 nad5 nad6 nad4L rrn5 Picozoa MS5584-11 Picozoa 8/12 Picozoa 22 Picozoa 43 Picozoa 11 A (ugc) C (gca) D (guc) E (uuc) F (gaa) G (gcc) G (ucc) H (gug) I (gau) K (uuu) L (uaa) L (uag) M (cau) N (guu) P (ugg) Q (uug) R (gcg) R (acg) R (ucg) R (ucu) S (gcu) S (uga) T (ugu) V (uac) W (cca) W (uca) Y (gua) Y (uua) Picozoa MS5584-11 Picozoa 8/12 Picozoa 43 Picozoa 22 Picozoa 11

Supplementary Figure 9: Complete and near complete mitochondrial genomes assembled from di- verse picozoan SAGs. A. Circular depictions of picozoan mitochondrial genomes compared to the published Picozoa MS584-11 sequence (Janouskovec et al. 2017). Mitochondrial contigs were annotated using mfannot with manual corrections as needed (http://megasun.bch.umontreal.ca/RNAweasel/). MtDNAs are represented as circular diagrams or broken circles if contigs could not be joined. For SAGs 8 and 12, the mitochondrial genome was inferred by stitching near-identical stretches together. Colour-coded genes: black, complex I; green, complex III; light green, complex IV; dark green, complex V; yellow, small ribosomal subunit proteins; red, large ribosomal subunit proteins; blue, tRNAs; pink, rnl and rns genes. B. gene complement of sequenced picozoan mitochondrial genomes. Top: protein coding and ribosomal RNA gene complement. Bottom: tRNA gene complement.

10 Arabidopsis thaliana (0) Pedospumella elongata (1) Cryptosporidium muris (2) Toxoplasma gondii (3) Chloropicon primus (4) Dinobryon sp UTEXLB2267 (4) Paraphysomonas bandaiensis (5) Helicosporidium sp ATCC50920 (8) Polytomella parva (8) Mallomonas sp CCMP3275 (9) Ochromonadales sp CCMP2298 (10) Leptocylindrus danicus (12) Thecamonas trahens (13) Rattus norvegicus (15) Phytophthora capsici (15) Galdieria sulphuraria (19) Guillardia theta (20)

Taxon Bigelowiella natans (23) Tetrahymena thermophila (23) Vitrella brassicaformis (24) Cryptomonas paramecium (25) Spumella bureschii JBL14 (25) Hematodinium sp SG-2012 (28) Dictyostelium discoideum (29) Rhodelphis (32) Emiliania huxleyi (32) Neurospora crassa (35) Paulinella chromatophora (49) Cyanophora paradoxa (55) Telonema subtile (62) Goniomonas pacifica (90) Alexandrium tamarense (93) Picozoa (99) 0 20 40 60 80 100 LGT

Supplementary Figure 10: Number of inferred lateral gene transfers (LGT) across a selection of 33 species. The species represent groups with a photosynthetic plastid (green), a non-photosynthetic plastid (blue), confirmed plastid loss (yellow) and no known plastid ancestry (black). These species serve as a com- parison to Picozoa (orange).

11 4 7 EU368003.1.1109_U_clone_FS01AA11_01Aug05_5m 100 EU368004.1.1126_U_clone_FS01AA94_01Aug05_5m 5 6 EU368020.1.1039_U_clone_FS04GA95_01Aug05_5m 100 DQ222876.1.1799_U_clone_RA000907.33 3 8 JF791041.1.1777_U_clone_7532 9 9 JX988764.1.1138_U_clone_PICOBI01F-L52R_10 9 6 79 0 3 KJ763213.1.1806_U_clone_SGUH612 COSAG02_NODE_9853_length_2092_cov_1534.832413 8 9 COSAG02_NODE_24963_length_672_cov_1437.080279 100 JX988758.1.1807_U_Picomonas_judraskeda 5 6 COSAG03_NODE_660_length_6398_cov_33.212415 5 4 SAG02_NODE_164_length_1182_cov_0.938135 4 7 COSAG06_NODE_7387_length_2521_cov_926.001652 6 5 KC488338.1.1714_U_clone_HL2SCM10.71 JN934893.1_Picobiliphyte_SAG_sp._MS609-66 9 3 JN934890.1_Picobiliphyte_SAG_MS584-5 7 8 100 HQ869261.1.1000_U_clone_SHBA597 9 1 HQ869362.1.935_U_clone_SHBA707 KJ762479.1.1805_U_clone_SGYH1057 5 2 JQ226352.1.1606_U_clone_SHAA389 3 6 KF031848.1.1765_U_clone_CC02A175.091 9 6 3 0 KJ173845.1.986_U_clone_DH117-1000m-C02 COSAG04_NODE_1053_length_8548_cov_1599.678542 KJ173847.1.992_U_clone_DH117-1000m-C10 4 6 HQ869099.1.906_U_clone_SHAX616 4 0 100 HQ869605.1.957_U_clone_SHBF578 HQ869692.1.905_U_clone_SHBF671 8 5 HQ869574.1.909_U_clone_SHBF544 6 3 7 9100 HM561168.1.984_U_clone_CFL146DB13 9 3 KC488345.1.1706_U_clone_HL5aSF04.93 JQ222911.1.1637_U_clone_SHAU435 KJ173838.1.862_U_clone_DH113-5m-D02 48 9 6 EU368037.1.1764_U_clone_EN351CTD039_30mN9 6 4 9 3 COSAG05_NODE_12267_length_474_cov_9412.762667 8 4 COSAG05_NODE_5341_length_1201_cov_7830.772232 JN934891.1_Picobiliphyte_SAG_sp._MS584-11 KJ173846.1.991_U_clone_DH117-1000m-C07 6 4 HQ868776.1.919_U_clone_SHAX1019 9 1 100 HQ868797.1.923_U_clone_SHAX1043 8 0 HQ868690.1.947_U_clone_SHAX927 100 COSAG01_NODE_11537_length_1910_cov_851.312535 4 2 6 1 SAG25_NODE_568_length_6882_cov_518.788589 9 9 KJ759275.1.1806_U_clone_SGYO1039 6 6 COSAG01_NODE_9630_length_2384_cov_183.060832 SAG25_NODE_1511_length_2866_cov_183.414840 KJ762972.1.1807_U_clone_SGUH1326 Picozoa 9 7 9 9 DQ222875.1.1801_U_clone_OR000415.159 7 4 100 JN934892.1_Picobiliphyte_SAG_sp._MS584-22 HQ867491.1.910_U_clone_SHAH476 9 9 HQ867421.1.875_U_clone_SHAC745 58 4 2 KF130491.1.1763_U_clone_ST8360.104 7 3 SAG22_NODE_175_length_16235_cov_67.112729 JX988767.1.1135_U_clone_PICOBI02F-L52R_He 9 9 DQ222874.1.1786_U_clone_HE001005.148 9 7 EU368021.1.1096_U_clone_FS04GA46_01Aug05_5m 100 AY426835.1.1803_U_clone_BL000921.8 9 4 SAG31_NODE_544_length_14245_cov_68.376644 3 7 HQ869075.1.930_U_clone_SHAX587 5 3 9 9 100 KJ173850.1.854_U_clone_DH117-1000m-D03 KJ173843.1.991_U_clone_DH116-100m-C03 JX840937.1.1271_U_clone_ARK_21 100 KJ763562.1.1796_U_clone_SGYP1354 8 8 SAG11_NODE_229_length_11945_cov_77.865187 5 2 DQ060528.1.800_U_clone_NOR50.25 8 9 100 5 5 DQ060527.1.1237_U_clone_NOR50.52 KC488340.1.1697_U_clone_HL5aSCM04.10 8 0 KC488342.1.1710_U_clone_HL5aSCM04.38 59 0 7 HM561172.1.953_U_clone_CFL119DB12 100 KJ762470.1.1800_U_clone_SGYH1041 HQ868882.1.878_U_clone_SHAX1135 KC488336.1.1682_U_clone_BBL1SF10.02 9 9 FN689854.1.826_U_clone_He040503_11A 9 6 9 5 HQ867389.1.887_U_clone_SHAC701 8 5 KJ759623.1.1791_U_clone_SGYO702 5 9 AY343928.1.1812_U_clone_He000803-72 100 HQ867420.1.880_U_clone_SHAC744 4 28 7 HQ867337.1.876_U_clone_SHAC623 HQ867471.1.868_U_clone_SHAC426 9 5 KC488339.1.1675_U_clone_HL2SF10.08 100 HQ867331.1.869_U_clone_SHAC614 5 6 6 4 HQ867442.1.871_U_clone_SHAC390 DQ060524.1.1778_U_clone_NW414.27 6 5 HQ869572.1.881_U_clone_SHBF542 7 1 HQ864893.1.880_U_clone_SGPX462 100 6 7 HQ866220.1.881_U_clone_SGSP644 4 9 HQ867427.1.876_U_clone_SHAC752 KC488334.1.1687_U_clone_BBL1SCM04.08 100 EU561759.1.879_U_clone_IND31.88 KJ759641.1.1788_U_clone_SGYO733 GU824414.1.1057_U_clone_AA5F13RM2D10 100 L28811.1.1763_U_strain_CCAP_977/2a|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Cryptomonas|Cryptomonas_paramecium 8 0 L28811.1.1763_U|18S_rRNA|nucleus|strain_CCAP_977/2a|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Cryptomonas|Cryptomonas_paramecium 100 7 2 AJ007285.1.1761_U_strain_CCMP_704|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Proteomonas|Proteomonas_sulcata AJ007285.1.1761_U|18S_rRNA|nucleus|strain_CCMP_704|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Proteomonas|Proteomonas_sulcata 100 HM126532.1.1732_U_strain_K-1487|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Rhodomonas|Rhodomonas_salina 2 5 HM126532.1.1732_U|18S_rRNA|nucleus|strain_K-1487|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Rhodomonas|Rhodomonas_salina 100 U53126.1.1756_U_strain_CCMP_325|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Hanusia|Hanusia_phi 100 U53126.1.1756_U|18S_rRNA|nucleus|strain_CCMP_325|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Hanusia|Hanusia_phi 100 5 4 9 64 9 X57162.1.1773_U_|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Guillardia|Guillardia_theta Cryptophyta X57162.1.1773_U|18S_rRNA|nucleus||Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Guillardia|Guillardia_theta 9 3 SAG33_NODE_446_length_7305_cov_7.971274 100 AM901350.1.1670_U_strain_CCMP_441|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Hemiselmis|Hemiselmis_andersenii AM901350.1.1670_U|18S_rRNA|nucleus|strain_CCMP_441|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Hemiselmis|Hemiselmis_andersenii 100 100 JF790986.1.1777_U_clone_1126|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Geminigera|Geminigera_cryophila JF790986.1.1777_U|18S_rRNA|nucleus|clone_1126|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptomonadales|Cryptomonadales_X|Geminigera|Geminigera_cryophila 100 AF508277.1.1721_U_strain_CCMP1869|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Goniomonadales|Goniomonadales_X|Goniomonas|Goniomonas_pacifica 7 6 AF508277.1.1721_U|18S_rRNA|nucleus|strain_CCMP1869|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Goniomonadales|Goniomonadales_X|Goniomonas|Goniomonas_pacifica 100 HQ191366.1.1830_U_clone_PA2009C5|Eukaryota|Hacrobia|Katablepharidophyta|Katablepharidaceae|Katablepharidales|Katablepharidales_X|Katablepharidales_XX|Katablepharidales_XX_sp. 8 8 GU068005.1.1774_U_clone_ESS241006.012|Eukaryota|Hacrobia|Katablepharidophyta|Katablepharidaceae|Katablepharidales|Katablepharidales_X|Katablepharidales_XX|Katablepharidales_XX_sp. 9 9 9 1 KJ925375.1.1690_U_clone_275D08|Eukaryota|Hacrobia|Katablepharidophyta|Katablepharidaceae|Katablepharidales|Katablepharidales_X|Katablepharidales_XX|Katablepharidales_XX_sp. 9 2 KJ762967.1.1799_U_clone_SGUH1318|Eukaryota|Hacrobia|Katablepharidophyta|Katablepharidaceae|Katablepharidales|Katablepharidales_X|Leucocryptos|Leucocryptos_marina KJ925380.1.1702_U_clone_275E02.|Eukaryota|Hacrobia|Katablepharidophyta|Katablepharidaceae|Katablepharidales|Katablepharidales_X|Katablepharidales_XX|Katablepharidales_XX_sp. Katablepharida 100 JP445963.602.2392_U_|Eukaryota|Hacrobia|Katablepharidophyta|Katablepharidaceae|Katablepharidales|Katablepharidales_X|Roombia|Roombia_truncata 7 2 7 5 6 7 JP445963.602.2392_U|18S_rRNA|nucleus||Eukaryota|Hacrobia|Katablepharidophyta|Katablepharidaceae|Katablepharidales|Katablepharidales_X|Roombia|Roombia_truncata GU823724.1.1189_U_clone_AA5F15RM2F06|Eukaryota|Hacrobia|Katablepharidophyta|Katablepharidaceae|Katablepharidales|Katablepharidales_X|Katablepharidales_XX|Katablepharidales_XX_sp. 4 9 X70803.22.1792_U|18S_rRNA|nucleus|strain_SAG_45.88|Eukaryota|Archaeplastida|Glaucophyta|Glaucocystophyceae|Glaucocystophytes|Glaucocystaceae|Glaucocystis|Glaucocystis_nostochinearum 100 X81901.1.1801_U|18S_rRNA|nucleus|strain_SAG_B_46.84|Eukaryota|Archaeplastida|Glaucophyta|Glaucocystophyceae|Glaucocystophytes|Glaucocystophytes_X|Gloeochaete|Gloeochaete_wittrockiana 5 8 AJ007275.1.1766_U|18S_rRNA|nucleus|strain_SAG_34.90|Eukaryota|Archaeplastida|Glaucophyta|Glaucocystophyceae|Glaucocystophytes|Cyanoptycaceae|Cyanoptyche|Cyanoptyche_gloeocystis Glaucophyta FR865776.2.1778_U|18S_rRNA|nucleus|strain_CCAP981/1|Eukaryota|Archaeplastida|Glaucophyta|Glaucocystophyceae|Glaucocystophytes|Cyanophoraceae|Cyanophora|Cyanophora_paradoxa 100 KC404120.1.1755_U|18S_rRNA|nucleus||Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Isochrysidales|Noelaerhabdaceae|Emiliania|Emiliania_huxleyi 100 KC404143.1.1755_U|18S_rRNA|nucleus||Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Isochrysidales|Noelaerhabdaceae|Gephyrocapsa|Gephyrocapsa_oceanica 2 6 HM149541.1.1795_U|18S_rRNA|nucleus|strain_SAG_13.92|Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Isochrysidales|Isochrysidaceae|Isochrysis|Isochrysis_galbana 3 4 AJ278035.1.1815_U|18S_rRNA|nucleus|strain_CCMP627|Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Phaeocystales|Phaeocystaceae|Phaeocystis|Phaeocystis_globosa 7 6 AM490984.1.1724_U|18S_rRNA|nucleus|strain_ALGO_TW16|Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Zygodiscales|Pontosphaeraceae|Scyphosphaera|Scyphosphaera_apsteinii 9 9 AJ544117.1.1716_U|18S_rRNA|nucleus||Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Coccolithales|Coccolithaceae|Coccolithus|Coccolithus_braarudii 9 2 AJ544116.1.1719_U|18S_rRNA|nucleus||Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Coccolithales|Calcidiscaceae|Calcidiscus|Calcidiscus_leptoporus 100 AJ246263.1.1808_U|18S_rRNA|nucleus|strain_von_Stosch|Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Coccolithales|Chrysotilaceae|Chrysotila|Chrysotila_carterae Haptophyta 2 9 AM491030.1.1787_U|18S_rRNA|nucleus|strain_UIO026___Q17_|Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Prymnesiales|Prymnesiaceae|Haptolina|Haptolina_ericina 100 9 5 9 9 L34671.1.1798_U|18S_rRNA|nucleus||Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Prymnesiales|Prymnesiaceae|Prymnesium|Prymnesium_parvum_f_patelliferum AM491015.1.1801_U|18S_rRNA|nucleus|strain_CCMP_1404|Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Prymnesiales|Prymnesiaceae|Dicrateria|Dicrateria_rotunda AM491020.1.1787_U|18S_rRNA|nucleus|strain_UIO044___TH2_|Eukaryota|Hacrobia|Haptophyta|Prymnesiophyceae|Prymnesiales|Chrysochromulinaceae|Chrysochromulina|Chrysochromulina_rotalis DQ531625.1.1791_U|18S_rRNA|nucleus|strain_AC15|Eukaryota|Hacrobia|Haptophyta|Pavlovophyceae|Pavlovales|Pavlovaceae|Exanthemachrysis|Exanthemachrysis_gayraliae 7 3 D86497.1.1790_U|18S_rRNA|nucleus|strain_UTEX_L193|Eukaryota|Archaeplastida|Chlorophyta|Chlorophyceae|Chlamydomonadales|Chlamydomonadales_X|Polytomella|Polytomella_parva 7 7 JN034412.1.1763_U|18S_rRNA|nucleus|specimen_CSMCRI_20110419014|Eukaryota|Archaeplastida|Chlorophyta|Ulvophyceae|Bryopsidales|Bryopsidales_X|Caulerpa|Caulerpa_lentillifera 7 8 100 M32703.1.1791_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Chlorophyta|Chlorophyceae|Chlamydomonadales|Chlamydomonadales_X|Chlamydomonas|Chlamydomonas_reinhardtii 7 6 X53904.1.1788_U|18S_rRNA|nucleus|strain_f._nagariensis 6 1 KJ756820.1.1790_U|18S_rRNA|nucleus|strain_CCAP_19/6B|Eukaryota|Archaeplastida|Chlorophyta|Chlorophyceae|Chlamydomonadales|Chlamydomonadales_X|Dunaliella|Dunaliella_tertiolecta 6 1 FN824385.1.1775_U|18S_rRNA|nucleus|strain_SAG112.80|Eukaryota|Archaeplastida|Chlorophyta|Chlorophyceae|Chaetophorales|Chaetophorales_X|Fritschiella|Fritschiella_tuberosa 9 7 AB162915.1.3271_G|18S_rRNA|nucleus|strain_KM2-ZK|Eukaryota|Archaeplastida|Chlorophyta|Trebouxiophyceae|Chlorellales|Chlorellales_X|Chlorella|Chlorella_variabilis X70802.22.1773_U|18S_rRNA|nucleus|strain_Ply_443|Eukaryota|Archaeplastida|Chlorophyta|Chlorodendrophyceae|Chlorodendrales|Chlorodendraceae|Tetraselmis|Tetraselmis_striata 9 2 AY165773.1.1774_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Chlorophyta|Ulvophyceae|Dasycladales|Dasycladales_X|Acetabularia|Acetabularia_acetabulum 8 8 U40921.1.1770_U|18S_rRNA|nucleus|strain_CCMP_1205|Eukaryota|Archaeplastida|Chlorophyta|Chloropicophyceae|Chloropicales|Chloropicaceae|Chloropicon|Chloropicon_primus 9 7 4 6 9 4 KF422628.1.1643_U|18S_rRNA|nucleus|strain_RCC2339|Eukaryota|Archaeplastida|Chlorophyta|Chloropicophyceae|Chloropicales|Chloropicaceae|Chloroparvula|Chloroparvula_japonica HM990659.1.1809_U|18S_rRNA|nucleus|clone_NE1_OUM_10|Eukaryota|Archaeplastida|Chlorophyta|Picocystophyceae|Picocystales|Picocystaceae|Picocystis|Picocystis_salinarum 6 4 X91264.1.1793_U|18S_rRNA|nucleus|strain_CCMP_1203|Eukaryota|Archaeplastida|Chlorophyta|Prasino-Clade-V|Pseudoscourfieldiales|Pycnococcaceae|Pycnococcus|Pycnococcus_provasolii AY425306.1.1758_U|18S_rRNA|nucleus|strain_RCC_499|Eukaryota|Archaeplastida|Chlorophyta|Nephroselmidophyceae|Nephroselmidales|Nephroselmidales_X|Nephroselmis|Nephroselmis_pyriformis Chlorophyta 7 4 8 3 CR954212.101402.103167_G|18S_rRNA|nucleus|strain_OTTH0595|Eukaryota|Archaeplastida|Chlorophyta|Mamiellophyceae|Mamiellales|Bathycoccaceae|Ostreococcus|Ostreococcus_tauri 100 KJ762910.1.1778_U|18S_rRNA|nucleus|clone_SGUH1189|Eukaryota|Archaeplastida|Chlorophyta|Mamiellophyceae|Mamiellales|Bathycoccaceae|Bathycoccus|Bathycoccus_prasinos 5 4 100 CP001575.879464.881247_U|18S_rRNA|nucleus|strain_RCC299|Eukaryota|Archaeplastida|Chlorophyta|Mamiellophyceae|Mamiellales|Mamiellaceae|Micromonas|Micromonas_commoda_A1 7 4 9 9 AB017128.1.1734_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Chlorophyta|Mamiellophyceae|Mamiellales|Mamiellaceae|Mantoniella|Mantoniella_antarctica KF615767.1.1654_U|18S_rRNA|nucleus|strain_CCMP3273|Eukaryota|Archaeplastida|Chlorophyta|Mamiellophyceae|Dolichomastigales|Crustomastigaceae|Crustomastix|Crustomastix_stigmatica 6 8 FN562449.1.1771_U|18S_rRNA|nucleus|strain_M1680|Eukaryota|Archaeplastida|Chlorophyta|Mamiellophyceae|Dolichomastigales|Dolichomastigaceae|Dolichomastix|Dolichomastix_tenuilepis 100 FN562443.1.1783_U|18S_rRNA|nucleus|strain_CCMP_726|Eukaryota|Archaeplastida|Chlorophyta|Pyramimonadales|Pyramimonadales_X|Pyramimonadales_XX|Pyramimonas|Pyramimonas_parkeae KF615764.1.1787_U|18S_rRNA|nucleus|strain_CCMP720|Eukaryota|Archaeplastida|Chlorophyta|Pyramimonadales|Pyramimonadales_X|Pyramimonadales_XX|Polyblepharides|Polyblepharides_amylifera 100 U40920.1.1796_U|18S_rRNA|nucleus|strain_CCMP_1220|Eukaryota|Archaeplastida|Chlorophyta|Palmophyllophyceae|Prasinococcales|Prasinococcales-Clade-B|Prasinoderma|Prasinoderma_coloniale U40919.1.1778_U|18S_rRNA|nucleus|strain_CCMP1407|Eukaryota|Archaeplastida|Chlorophyta|Palmophyllophyceae|Prasinococcales|Prasinococcales-Clade-A|Prasinococcus|Prasinococcus_capsulatus 8 1 ACUP01007508.35654.37464_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Glycine|Glycine_max 4 5 X16077.60.1902_U|18S_rRNA|nucleus|clone_ATR3|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Arabidopsis|Arabidopsis_thaliana 8 0 AC184066.23690.25500_U|18S_rRNA|nucleus|clone_Pop1-110G16|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Populus|Populus_trichocarpa 9 1 9 9 AASG02007143.7906.9773_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Ricinus|Ricinus_communis AM478788.348.2246_U|18S_rRNA|nucleus|clone_ENTAV_115|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Vitis|Vitis_vinifera JF966545.1.1748_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Persea|Persea_americana 4 1 7 4 9 8 ADDN01001476.2953.4766_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Brachypodium|Brachypodium_distachyon 4 7 6 6 6 9 AY552749.1.1014_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Hordeum|Hordeum_vulgare 100100 AAAA02046270.109.1957_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Oryza|Oryza_sativa AC213764.149505.151391_U|18S_rRNA|nucleus|clone_CH201-469G12|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Zea|Zea_mays 6 1 ABXC01003371.303870.305894_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Sorghum|Sorghum_bicolor U42497.1.1741_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Amborella|Amborella_trichopoda 100 8 6 AF207059.1.1750_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Welwitschia|Welwitschia_mirabilis Streptophy 9 7 AC241294.94037.95852_U|18S_rRNA|nucleus|clone_PT_7Ba2900I02|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Pinus|Pinus_taeda D16448.1.1732_U|18S_rRNA|nucleus|clone_clones_1-1 100 3 36 5 U18628.1.1754_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Pteridium|Pteridium_aquilinum 9 9 X81963.1.1811_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Psilotum|Psilotum_nudum ADFJ01003580.8656.10787_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Selaginella|Selaginella_moellendorffii 4 6 8 8 AC158196.4669.6492_U|18S_rRNA|nucleus|clone_JGIASYB-1A11|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Physcomitrella|Physcomitrella_patens AY342317.10341.12160_U|18S_rRNA|nucleus|strain_E|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Marchantia|Marchantia_polymorpha 9 9 AF115439.1.2167_G|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Streptophyta|Zygnemophyceae|Zygnemophyceae_X|Zygnemophyceae_XX|Cylindrocystis|Cylindrocystis_brebissonii 6 4 AJ428070.1.1749_U|18S_rRNA|nucleus|strain_SVCK_48|Eukaryota|Archaeplastida|Streptophyta|Zygnemophyceae|Zygnemophyceae_X|Zygnemophyceae_XX|Netrium|Netrium_digitus X68825.1.1807_U|18S_rRNA|nucleus|strain_SAG_110.80|Eukaryota|Archaeplastida|Streptophyta|Coleochaetophyceae|Coleochaetophyceae_X|Coleochaetophyceae_XX|Coleochaete|Coleochaete_scutata 6 3 AF032747.1.1761_U|18S_rRNA|nucleus|strain_X-152|Eukaryota|Archaeplastida|Streptophyta|Charophyceae|Charophyceae_X|Charophyceae_XX|Chara|Chara_vulgaris AJ250109.1.1782_U|18S_rRNA|nucleus|strain_NIES_475|Eukaryota|Archaeplastida|Streptophyta|Mesostigmatophyceae|Mesostigmatophyceae_X|Mesostigmatophyceae_XX|Mesostigma|Mesostigma_viride 100 MK966713.1_Rhodelphis_limneticus_strain_Colp-38 6 9 MK966712.1_Rhodelphis_marinus_strain_Colp-29 Rodelphidia AB508339.1.1724_U|18S_rRNA|nucleus||Eukaryota|Hacrobia|Hacrobia_X|Hacrobia_XX|Hacrobia_XXX|Hacrobia_XXXX|Palpitomonas|Palpitomonas_bilix 4 4 GU220392.1.1879_U|18S_rRNA|nucleus||Eukaryota|Stramenopiles|Ochrophyta|Chrysophyceae|Chrysophyceae_X|Chrysophyceae_Clade-F|Paraphysomonas|Paraphysomonas_vestita 4 7 AF109322.1.1762_U|18S_rRNA|nucleus|strain_Hflag|Eukaryota|Stramenopiles|Ochrophyta|Chrysophyceae|Chrysophyceae_X|Chrysophyceae_Clade-F|Paraphysomonas|Paraphysomonas_bandaiensis 100 EF432518.1.1793_U|18S_rRNA|nucleus|clone_C1|Eukaryota|Stramenopiles|Ochrophyta|Chrysophyceae|Chrysophyceae_X|Chrysophyceae_Clade-F|Paraphysomonas|Paraphysomonas_imperforata 9 8 4 7 EF023425.1.1776_U|18S_rRNA|nucleus|clone_Amb_18S_766|Eukaryota|Stramenopiles|Ochrophyta|Chrysophyceae|Chrysophyceae_X|Chrysophyceae_Clade-C|Spumella|Spumella_vulgaris AF123285.1.1777_U|18S_rRNA|nucleus|strain_CCMP263|Eukaryota|Stramenopiles|Ochrophyta|Chrysophyceae|Chrysophyceae_X|Chrysophyceae_Clade-B2|Chromulina_Clade-B2|Chromulina_nebulosa 4 9 KF925343.1.1655_U|18S_rRNA|nucleus|specimen_NCMA 100 DQ191680.1.2121_U|18S_rRNA|nucleus|strain_CCMP_2191|Eukaryota|Stramenopiles|Ochrophyta|Raphidophyceae|Raphidophyceae_X|Raphidophyceae_XX|Chattonella|Chattonella_subsalsa 7 0 DQ191681.1.2105_U|18S_rRNA|nucleus|strain_CCMP_2393|Eukaryota|Stramenopiles|Ochrophyta|Raphidophyceae|Raphidophyceae_X|Raphidophyceae_XX|Heterosigma|Heterosigma_akashiwo 2 8 FN564440.1.1804_U|18S_rRNA|nucleus|strain_Ec393|Eukaryota|Stramenopiles|Ochrophyta|Phaeophyceae|Phaeophyceae_X|Phaeophyceae_XX|Ectocarpus|Ectocarpus_siliculosus 100 AF438324.1.1768_U|18S_rRNA|nucleus|strain_CCMP1144|Eukaryota|Stramenopiles|Ochrophyta|Pinguiophyceae|Pinguiochrysidales|Pinguiochrysidaceae|Pinguiococcus|Pinguiococcus_pyrenoidosus 9 8 KC583001.1.1813_U|18S_rRNA|nucleus|clone_RS.12f.10m.70|Eukaryota|Stramenopiles|Ochrophyta|Pinguiophyceae|Pinguiochrysidales|Pinguiochrysidaceae|Phaeomonas|Phaeomonas_parva 100 AY254857.1.1771_U|18S_rRNA|nucleus|strain_RCC_446|Eukaryota|Stramenopiles|Ochrophyta|Dictyochophyceae|Dictyochophyceae_X|Florenciellales|Florenciella|Florenciella_parvula 100 AM075624.1.1794_U|18S_rRNA|nucleus|strain_UIO_110|Eukaryota|Stramenopiles|Ochrophyta|Dictyochophyceae|Dictyochophyceae_X|Florenciellales|Pseudochattonella|Pseudochattonella_farcimen 4 4 U14387.1.1810_U|18S_rRNA|nucleus||Eukaryota|Stramenopiles|Ochrophyta|Dictyochophyceae|Dictyochophyceae_X|Pedinellales|Pseudopedinella|Pseudopedinella_elastica 4 6 100 LC009879.1.2717_U|18S_rRNA|nucleus|strain_URACC_SH6-A|Eukaryota|Stramenopiles|Ochrophyta|Pelagophyceae|Pelagomonadales|Pelagomonadaceae|Pelagomonas|Pelagomonas_calceolata U40258.1.2236_U|18S_rRNA|nucleus|strain_TBA|Eukaryota|Stramenopiles|Ochrophyta|Pelagophyceae|Sarcinochrysidales|Sarcinochrysidaceae|Aureoumbra|Aureoumbra_lagunensis AF045043.1.1792_U|18S_rRNA|nucleus|strain_CCMP535|Eukaryota|Stramenopiles|Ochrophyta|Eustigmatophyceae|Eustigmatophyceae_X|Eustigmatophyceae_XX|Nannochloropsis|Nannochloropsis_granulata 100 6 9 AY485504.1.2243_U|18S_rRNA|nucleus|strain_CCMP393|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Polar-centric-Mediophyceae|Extubocellulus|Extubocellulus_spinifer 7 9 HQ912568.1.1793_U|18S_rRNA|nucleus|strain_CCMP497|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Polar-centric-Mediophyceae|Minutocellus|Minutocellus_polymorphus Stramenopila 9 0 100 KC771208.1.1802_U|18S_rRNA|nucleus|clone_WC-13-MC1244-OTU-2|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Polar-centric-Mediophyceae|Thalassiosira|Thalassiosira_antarctica AB630054.1.1798_U|18S_rRNA|nucleus|strain_FOS010|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Polar-centric-Mediophyceae|Skeletonema|Skeletonema_marinoi 6 2 AY485446.1.1784_U|18S_rRNA|nucleus|strain_RR|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Polar-centric-Mediophyceae|Chaetoceros|Chaetoceros_debilis 4 4 100 U18241.1.1773_U|18S_rRNA|nucleus||Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Raphid-pennate|Pseudo-nitzschia|Pseudo-nitzschia_multiseries 8 7 5 4 100 DR026462.36.1826_U|18S_rRNA|nucleus|clone_FcylESTa38f08.s1|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Raphid-pennate|Fragilariopsis|Fragilariopsis_cylindrus 100 GQ452862.1.1803_U|18S_rRNA|nucleus|strain_KMMCC_B-414|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Raphid-pennate|Phaeodactylum|Phaeodactylum_tricornutum 9 9 9 6 AJ535181.1.1798_U|18S_rRNA|nucleus|clone_p433|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Radial-centric-basal-Coscinodiscophyceae|Proboscia|Proboscia_alata AJ535175.1.1805_U|18S_rRNA|nucleus|strain_KM_9950|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Radial-centric-basal-Coscinodiscophyceae|Leptocylindrus|Leptocylindrus_danicus AF167153.1.1799_U|18S_rRNA|nucleus|strain_RCC210|Eukaryota|Stramenopiles|Ochrophyta|Bolidophyceae|Parmales|Triparmaceae|Triparma|Triparma_eleuthera BT032234.1.1815_U|18S_rRNA|nucleus|clone_CBOT157-J12|Eukaryota|Stramenopiles|Pseudofungi|Oomycota|Oomycota_X|Peronosporales|Phytophthora|Phytophthora_capsici HM042904.1.1758_U|18S_rRNA|nucleus||Eukaryota|Stramenopiles|Sagenista|Labyrinthulomycetes|Thraustochytriales|Thraustochytriaceae|Aurantiochytrium|Aurantiochytrium_limacinum 7 7 8 3 X70809.1.1793_U|18S_rRNA|nucleus|strain_Grell__Tunisia_|Eukaryota|Rhizaria|Cercozoa|Chlorarachniophyceae|Chlorarachnida|Chlorarachnida_X|Chlorarachnion|Chlorarachnion_reptans 6 1 100 KJ763172.1.1800_U|18S_rRNA|nucleus|clone_SGUH550|Eukaryota|Rhizaria|Cercozoa|Chlorarachniophyceae|Chlorarachnida|Chlorarachnida_X|Partenskyella|Partenskyella_glossopodia 100 JF826444.1.1746_U|18S_rRNA|nucleus|strain_LEX01|Eukaryota|Rhizaria|Cercozoa|Chlorarachniophyceae|Chlorarachnida|Chlorarachnida_X|Lotharella|Lotharella_globosa 7 2 AF054832.1.1762_U|18S_rRNA|nucleus|strain_CCMP_621|Eukaryota|Rhizaria|Cercozoa|Chlorarachniophyceae|Chlorarachnida|Chlorarachnida_X|Bigelowiella|Bigelowiella_natans Cercozoa 8 8 FJ456918.1.1815_U|18S_rRNA|nucleus|strain_FK01|Eukaryota|Rhizaria|Cercozoa|Filosa-Imbricatea|Euglyphida|Paulinellidae|Paulinella|Paulinella_chromatophora U18981.1.3026_G|18S_rRNA|nucleus||Eukaryota|Rhizaria|Cercozoa|Endomyxa-Phytomyxea|Plasmodiophorida|Plasmodiophoridae|Plasmodiophora|Plasmodiophora_brassicae X00601.1766.3662_U|18S_rRNA|nucleus||Eukaryota|Amoebozoa|Conosa|Mycetozoa-Dictyostelea|Dictyosteliida|Dictyosteliida-Group-IV|Dictyostelium-Group-IV|Dictyostelium_discoideum 100 AB190459.1.1746_U|18S_rRNA|nucleus|strain_N/A 9 1 KF559357.1.1749_U|18S_rRNA|nucleus||Eukaryota|Alveolata|Apicomplexa|Coccidiomorphea|Piroplasmorida|Theileriidae|Theileria|Theileria_equi 7 4 AF096498.1.1747_U|18S_rRNA|nucleus|strain_H.H-34|Eukaryota|Alveolata|Apicomplexa|Coccidiomorphea|Eimeriida|Sarcocystidae|Toxoplasma1|Hammondia_hammondi 7 8 5 6 7 9 EF666482.1.1787_U|18S_rRNA|nucleus||Eukaryota|Alveolata|Apicomplexa|Gregarinomorphea|Neogregarinorida|Actinocephalidae|Ascogregarina|Ascogregarina_taiwanensis 6 7 DQ093796.1.1625_U|18S_rRNA|nucleus||Eukaryota|Alveolata|Apicomplexa|Gregarinomorphea|Eugregarinorida|Lecudinidae|Lankesteria|Lankesteria_abbotti AF280076.1.1787_U|18S_rRNA|nucleus|strain_ATCC_50640|Eukaryota|Alveolata|Apicomplexa|Colpodellidea|Colpodellida|Colpodellaceae|Voromonas|Voromonas_pontica JN986788.1.1711_U|18S_rRNA|nucleus||Eukaryota|Alveolata|Apicomplexa|Colpodellidea|Colpodellida|Chromeraceae|Chromera|Chromera_velia 7 7 HF674441.1.1727_U|18S_rRNA|nucleus|strain_AMJJ1|Eukaryota|Alveolata|Dinoflagellata|Dinophyceae|Gymnodiniales|Gymnodiniaceae|Amphidinium|Amphidinium_massartii 9 9 7 1 9 7 DQ444290.523.2323_U|18S_rRNA|nucleus|strain_CCMP1719|Eukaryota|Alveolata|Dinoflagellata|Dinophyceae|Gonyaulacales|Goniodomataceae|Alexandrium|Alexandrium_tamarense 2 5 AF231804.1.1795_U|18S_rRNA|nucleus||Eukaryota|Alveolata|Dinoflagellata|Dinophyceae|Peridiniales|Kryptoperidiniaceae|Kryptoperidinium|Kryptoperidinium_foliaceum Alveolata DQ785882.606.2409_U|18S_rRNA|nucleus|strain_GnCt01|Eukaryota|Alveolata|Dinoflagellata|Dinophyceae|Gymnodiniales|Gymnodiniaceae|Gymnodinium|Gymnodinium_catenatum 7 1 7 9 AB033717.1.1749_U|18S_rRNA|nucleus|strain_NIES494|Eukaryota|Alveolata|Dinoflagellata|Oxyrrhea|Oxyrrhinales|Oxyrrhinaceae|Oxyrrhis|Oxyrrhis_marina 100 AF497479.1251.3059_U|18S_rRNA|nucleus|strain_TXsc|Eukaryota|Alveolata|Perkinsea|Perkinsida|Perkinsida_X|Perkinsida_XX|Perkinsus|Perkinsus_marinus 9 9 AY305326.1543.3351_U|18S_rRNA|nucleus|strain_ATCC_50807|Eukaryota|Alveolata|Perkinsea|Perkinsida|Perkinsida_X|Perkinsida_XX|Perkinsus|Perkinsus_chesapeaki 9 8 AF508773.1.1770_U|18S_rRNA|nucleus||Eukaryota|Alveolata|Ciliophora|Spirotrichea|Hypotrichia|Oxytrichidae|Stylonychia|Stylonychia_lemnae 7 5 X56165.1.1753_U|18S_rRNA|nucleus|strain_ATCC_30377|Eukaryota|Alveolata|Ciliophora|Oligohymenophorea|Hymenostomatia|Tetrahymenida|Tetrahymena|Tetrahymena_thermophila 7 8 KJ598081.1.1728_U|18S_rRNA|nucleus|clone_Colp-62|Eukaryota|Protalveolata|Protalveolata_X|Colponemea|Colponemida|Colponemidae|Colponema|Colponema_vietnamica 7 5 U25439.1.1777_U|18S_rRNA|nucleus|strain_brown_form|Eukaryota|Archaeplastida|Rhodophyta|Florideophyceae|Gigartinales|Gigartinales_X|Eucheuma|Eucheuma_denticulatum 100 100 Z14141.1.1774_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Rhodophyta|Florideophyceae|Gigartinales|Gigartinales_X|Furcellaria|Furcellaria_lumbricalis 100 DQ317002.1.1780_U|18S_rRNA|nucleus|specimen_EMBLCH307016|Eukaryota|Archaeplastida|Rhodophyta|Florideophyceae|Gigartinales|Gigartinales_X|Chondrus|Chondrus_crispus 7 2 Z14142.1.1771_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Rhodophyta|Florideophyceae|Colaconematales|Colaconematales_X|Palmaria|Palmaria_palmata AF076995.21.2240_G|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Rhodophyta|Florideophyceae|Hildenbrandiales|Hildenbrandiales_X|Hildenbrandia|Hildenbrandia_rubra 6 4 AF168624.1.1741_U|18S_rRNA|nucleus|strain_UTEX_LB_2427|Eukaryota|Archaeplastida|Rhodophyta|Rhodellophyceae|Rhodellales|Rhodellales_X|Rhodella|Rhodella_violacea 7 9 100 HQ687584.1.2287_G|18S_rRNA|nucleus|specimen_WELT_A024414|Eukaryota|Archaeplastida|Rhodophyta|Bangiophyceae|Bangiales|Bangiaceae|Porphyra|Porphyra_umbilicalis DQ227856.1.3314_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Rhodophyta|Bangiophyceae|Bangiales|Bangiaceae|Pyropia|Pyropia_yezoensis 100 AB090833.1.1781_U|18S_rRNA|nucleus|strain_61D|Eukaryota|Archaeplastida|Rhodophyta|Bangiophyceae|Cyanidiales|Cyanidiales_X|Cyanidium|Cyanidium_caldarium 4 6 AB158485.2739.4547_U|18S_rRNA|nucleus|strain_10D|Eukaryota|Archaeplastida|Rhodophyta|Bangiophyceae|Cyanidiales|Cyanidiales_X|Cyanidioschyzon|Cyanidioschyzon_merolae Rhodophyta 6 9 JX511996.1.1781_U|18S_rRNA|nucleus|strain_BR-CI|Eukaryota|Archaeplastida|Rhodophyta|Compsopogonophyceae|Compsopogonales|Compsopogonales_X|Compsopogon|Compsopogon_caeruleus 8 3 KF925342.1.1620_U|18S_rRNA|nucleus|specimen_NCMA 3 0 100 100 KF422614.1.2272_U|18S_rRNA|nucleus|strain_CCMP3278|Eukaryota|Archaeplastida|Rhodophyta|Porphyridiophyceae|Porphyridiales|Porphyridiales_X|Timspurckia|Timspurckia_oligopyrenoides EU818942.1.1773_U|18S_rRNA|nucleus|strain_CCAP1380-3|Eukaryota|Archaeplastida|Rhodophyta|Porphyridiophyceae|Porphyridiales|Porphyridiales_X|Porphyridium|Porphyridium_purpureum 5 7 AY617151.1.1713_U|18S_rRNA|nucleus||Eukaryota|Archaeplastida|Rhodophyta|Stylonematophyceae|Porphyridiales-2|Stylonematales-Group-I|Purpureofilum|Purpureofilum_apyrenoidigerum 9 6 6 6 AF342750.1.1789_U|18S_rRNA|nucleus|strain_SAG_116.79|Eukaryota|Archaeplastida|Rhodophyta|Stylonematophyceae|Porphyridiales-2|Stylonematales-Group-II|Rhodosorus|Rhodosorus_marinus AB091230.1.1776_U|18S_rRNA|nucleus|strain_SAG21.92|Eukaryota|Archaeplastida|Rhodophyta|Bangiophyceae|Cyanidiales|Cyanidiales_X|Galdieria|Galdieria_sulphuraria 7 9 L42528.1.1787_U|18S_rRNA|nucleus||Eukaryota|Opisthokonta|Mesomycetozoa|Corallochytrea|Corallochytrida|Corallochytridae|Corallochytrium|Corallochytrium_limacisporum 8 6 Y19155.1.1797_U|18S_rRNA|nucleus|strain_ATCC_32708|Eukaryota|Opisthokonta|Mesomycetozoa|Ichthyosporea|Ichthyosphonida|Ichthyophonidae_Amoebidianae|Amoebidium|Amoebidium_parasiticum 3 5 L29455.1.1809_U|18S_rRNA|nucleus||Eukaryota|Opisthokonta|Mesomycetozoa|Ichthyosporea|Rhynosporida|Rhynosporidae_Sphaerothecideanae|Sphaerothecum|Sphaerothecum_destruens 8 0 ACFS01000464.73319.75121_U|18S_rRNA|nucleus||Eukaryota|Opisthokonta|Mesomycetozoa|Filasterea|Capsasporida|Capsasporidae|Capsaspora|Capsaspora_owczarzaki 100 M11188.1.1920_U|18S_rRNA|nucleus||Eukaryota|Opisthokonta|Metazoa|Craniata|Craniata_X|Mammalia|Rattus|Rattus_norvegicus Opisthokonta 4 2 3 7 7 6 CABZ01108928.4.1948_U|18S_rRNA|nucleus||Eukaryota|Opisthokonta|Metazoa|Craniata|Craniata_X|Teleostei|Danio|Danio_rerio FJ360521.1885.3680_U|18S_rRNA|nucleus||Eukaryota|Opisthokonta|Fungi|Ascomycota|Pezizomycotina|Sordariomycetes|Neurospora|Neurospora_crassa 1 6 FJ816018.1.1805_U|18S_rRNA|nucleus|strain_ATCC_38817|Eukaryota|Opisthokonta|Opisthokonta_X|Fonticulea|Fonticulida|Fonticulidae|Fonticula|Fonticula_alba 7 9 9 2 JQ340335.1.1776_U|18S_rRNA|nucleus|strain_il19|Eukaryota|Apusozoa|Hilomonadea|Planomonadida|Planomonadidae|Planomonadidae_Group-1|Fabomonas|Fabomonas_tropica JQ340331.1.1817_U|18S_rRNA|nucleus|strain_ncfw|Eukaryota|Apusozoa|Hilomonadea|Planomonadida|Planomonadidae|Planomonadidae_Group-2|Nutomonas|Nutomonas_longa AJ564771.1.1831_U|18S_rRNA|nucleus||Eukaryota|Hacrobia|Telonemia|Telonemia_X|Telonemia_XX|Telonemia-Group-1|Telonema-Group-1|Telonema_subtile 9 9 AF153206.1.1748_U|18S_rRNA|nucleus||Eukaryota|Amoebozoa|Breviatea|Breviatea_X|Breviatea_XX|Breviata-lineage|Breviata|Breviata_anathema 8 2 KC433554.1.1820_U|18S_rRNA|nucleus|strain_PCbi66|Eukaryota|Opisthokonta|Opisthokonta_X|Opisthokonta_XX|Opisthokonta_XXX|Opisthokonta_XXXX|Pygsuia|Pygsuia_biforma GU001154.1.1778_U|18S_rRNA|nucleus|strain_CCAP1946/1|Eukaryota|Apusozoa|Mantamonadidea|Mantamonadida|Mantamonadida_X|Mantamonadida_XX|Mantamonas|Mantamonas_plastica 8 4 100 AB263123.1.1704_U|18S_rRNA|nucleus||Eukaryota|Excavata|Metamonada|Fornicata|Fornicata_X|Carpediomonas-like|Dysnectes|Dysnectes_brevis 8 9 AY117416.1.1763_U|18S_rRNA|nucleus||Eukaryota|Excavata|Metamonada|Fornicata|Fornicata_X|Carpediomonas-like|Carpediemonas|Carpediemonas_membranifera 6 2 ADVD01001051.10304.12136_U|18S_rRNA|nucleus||Eukaryota|Apusozoa|Apusomonadidae|Apusomonadidae_Group-2|Apusomonadidae_Group-2_X|Apusomonadidae_Group-2_XX|Thecamonas|Thecamonas_trahens 8 8 9 1 AB686266.1.1858_U|18S_rRNA|nucleus|strain_YPF923|Eukaryota|Apusozoa|Hilomonadea|Planomonadida|Planomonadidae|Planomonadidae_X|Rigifila|Rigifila_ramosa AF420478.1.1737_U|18S_rRNA|nucleus||Eukaryota|Apusozoa|Apusomonadidae|Apusomonadidae_Group-4|Apusomonadidae_Group-4_X|Apusomonadidae_Group-4_XX|Diphylleia|Diphylleia_rotans AY117420.1.1867_U|18S_rRNA|nucleus|strain_ATCC_50310|Eukaryota|Excavata|Malawimonadidae|Malawimonadidae_X|Malawimonadidae_XX|Malawimonadidae_XXX|Malawimonas|Malawimonas_jakobiformis AY965870.1.1850_U|18S_rRNA|nucleus||Eukaryota|Excavata|Discoba|Jakobida|Jakobida_X|Jakobidae|Andalucia|Andalucia_godoyi 6 0 AF053089.1.1843_U|18S_rRNA|nucleus||Eukaryota|Excavata|Discoba|Jakobida|Jakobida_X|Jakobidae|Reclinomonas|Reclinomonas_americana 100 AF112871.1.2394_U|18S_rRNA|nucleus|specimen_UTEX__512|Eukaryota|Excavata|Discoba|Euglenozoa|Euglenida|Euglenales|Euglena|Euglena_longa 100 100 M12677.1.2305_U|18S_rRNA|nucleus||Eukaryota|Excavata|Discoba|Euglenozoa|Euglenida|Euglenales|Euglena|Euglena_gracilis 5 0 AY082988.1.2503_U|18S_rRNA|nucleus|clone_RT8n7|Eukaryota|Excavata|Discoba|Euglenozoa|Euglenida|Euglenales|Euglena|Euglena_mutabilis FJ719618.1.2210_U|18S_rRNA|nucleus|strain_Masan|Eukaryota|Excavata|Discoba|Euglenozoa|Euglenida|Eutreptiales|Eutreptiella|Eutreptiella_gymnastica AB576851.1.1984_U|18S_rRNA|nucleus|strain_TKB-055|Eukaryota|Excavata|Discoba|Tsukubamonadidae|Tsukubamonadidae_X|Tsukubamonadidae_XX|Tsukubamonas|Tsukubamonas_globosa 100 M81842.61.1631_U|18S_rRNA|nucleus|strain_CROP-1|Eukaryota|Excavata|Metamonada|Parabasalia|Cristamonadida|Tritrichomonadidae|Tritrichomonas|Tritrichomonas_foetus 6 0 AAHC01002997.1925.3504_U|18S_rRNA|nucleus||Eukaryota|Excavata|Metamonada|Parabasalia|Trichomonadida|Trichomonadidae|Trichomonas|Trichomonas_vaginalis 9 6 HQ898857.1.3325_G|18S_rRNA|nucleus|strain_AS12B|Eukaryota|Excavata|Discoba|Heterolobosea|Heterolobosea_X|Pharyngomonaceae|Pharyngomonas|Pharyngomonas_kirbyi AB298288.901.2920_U|18S_rRNA|nucleus|strain_NEG-M|Eukaryota|Excavata|Discoba|Heterolobosea|Heterolobosea_X|Vahlkampfiidae|Naegleria|Naegleria_gruberi

0.4

Supplementary Figure 11: Maximum Likelihood tree of the 18S rRNA gene from the individual SAG assemblies and an extended number of reference sequences from Picozoa and other major eukaryotic groups from the PR2 database. The tree was reconstructed under the model GTR+R5+F.

12 inwr osdrda ela h eut o l hs 0asmle obnd o h obndvle a value, combined the assembly. For one combined. least assemblies at in 10 complete these was all it for if results complete the considered as Fragmented was well BUSCO Complete, as (Missing, considered categories were BUSCO SAGs/Co-SAGs. tion selected different all of for Boxplots Duplicated) and 13: Figure Supplementary estimated as SAGs picozoan initial 43 assemblies. for the ANI between pairwise showing FastANI. Heatmap with 12: Figure Supplementary

% of BUSCOs 100 20 40 60 80 0 SAG43 SAG42 SAG41 SAG40 SAG39 SAG38 SAG36 SAG35 SAG33 SAG32 SAG31 SAG30 SAG29 SAG28 SAG27 SAG26 SAG25 SAG24 SAG23 SAG22 SAG21 SAG20 SAG19 SAG18 SAG17 SAG16 SAG15 SAG14 SAG13 SAG12 SAG11 SAG09 SAG08 SAG04 SAG03 SAG02 SAG01 u oteicmltns fteSG,mn N ausaezr,sneteei ooverlap no is there since zero, are values ANI many SAGs, the of incompleteness the to Due

SAG01

Missing SAG02

SAG03

SAG04

SAG08

SAG09

SAG11

SAG12

SAG13

SAG14

SAG15

Duplicated SAG16

SAG17

SAG18

SAG19

SAG20 nySG htwr sdfrPyoeoi reconstruc- Phylogenomic for used were that SAGs Only

13 SAG21

Status SAG22

SAG23

SAG24

SAG25

SAG26 Fragmented

SAG27

SAG28

SAG29

SAG30

SAG31

SAG32

SAG33

SAG35

SAG36

SAG38

SAG39 Complete SAG40

Dataset SAG41

Combined (CO)SAGs SAG42

SAG43 80 85 90 95 100 100 status eukaryotic prokaryotic/viral 80

60 length [%] 40

20

0

SAG02SAG03SAG05SAG07SAG10SAG11SAG22SAG25SAG31SAG33SAG37 COSAG01COSAG02COSAG03COSAG04COSAG05COSAG06 SAG

Supplementary Figure 14: Contamination estimate for each of the 17 final SAGs/Co-SAGs. All proteins were subjected to a DIAMOND blastp search against the ncbi NR database. If 60% of all proteins predicted from a contig only showed significant hits to prokaryotes or viruses, the contig was considered a putative contamination. Values correspond to fractions of contaminated/clean contigs of the total assembly length.

14 99 Archaeplastida-Viridiplantae_Chlorophyta_N_A_Pyramimonadales_N_A_Pyramimonas_parkeae_CCMP726 100 Archaeplastida-Viridiplantae_Chlorophyta_N_A_Prasinococcales_N_A_Prasinoderma_singulare_RCC927 100 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Volvocaceae_Volvox_carteri_N_A 100 Archaeplastida-Viridiplantae_Streptophyta_Bryopsida_Funariales_Funariaceae_Physcomitrella_patens_N_A 100 Archaeplastida-Viridiplantae_Streptophyta_N_A_Brassicales_Brassicaceae_Arabidopsis_thaliana_TAIR10 98 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_Gloeochaetales_Gloeochaetaceae_Gloeochaete_wittrockiana_SAG46.84 100 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N_A_Cyanophoraceae_Cyanophora_paradoxa_N_A Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N_A_N_A_Cyanoptyche_gloeocystis_SAG4.97 99 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Geminigera_merged_sp_cryophila 100 Cryptista_Cryptophyta_Cryptophyta_N_A_N_A_Cryptophyceae_sp_merged_CCMP2293_N_A 100 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Chroomonadaceae_Chroomonas_mesostigmatica_CCMP1168 100 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_pacifica_merged_CCMP1869_N_A 100 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_merged_sp_avonlea Cryptista_Katablepharida_Katablepharidophyta_N_A_N_A_Roombia_truncata_N_A Cryptista_Palpitia_N_A_N_A_N_A__Palpitomonas_bilix_merged_NIES-2562_N_A 100 100 Archaeplastida-Rhodophyta_Rhodophyta_Compsopogonophyceae_Compsopogonales_Compsopogonaceae_Compsopogon_caeruleus_SAG36.94 98 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Porphyridium_purpureum_N_A 100 Archaeplastida-Rhodophyta_Rhodophyta_Stylonematophyceae_Stylonematales_Stylonemataceae_Rhodosorus_marinus_merged_UTEXLB2760_CCMP769 100 100 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gigartinales_Gigartinaceae_Chondrus_crispus_N_A Archaeplastida-Rhodophyta_Rhodophyta_Bangiophyceae_Bangiales_Bangiaceae_merged_Porphyra_Pyropia 100 100 Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Galdieria_sulphuraria_N_A Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Cyanidioschyzon_merolae_N_A 100 Archaeplastida-Rhodelphea_N_A_N_A_Rhodelphida_Rhodelphidae_Rhodelphis_marinus_merged_Colp29_N_A 100 Archaeplastida-Rhodelphea_N_A_N_A_Rhodelphida_Rhodelphidae_Rhodelphis_limneticus_N_A 100 Picozoa_Picozoa_N_A_N_A_N_A_N_A_N_A__merged_COSAG02_COSAG03_COSAG04_COSAG06 100 Picozoa_Picozoa_N_A_N_A_N_A_merged_Picobiliphyte_sp_MS584-11_COSAG05_COSAG01_SAG25 Picozoa_Picozoa_N_A_N_A_N_A_N_A_N_A_merged_SAG22_SAG31_SAG11 100 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_merged_C15_C1 100 Alveolata_Dinophyta_Dinophyceae_Oxyrrhinales_Oxyrrhinaceae_Oxyrrhis_marina_merged_CCMP1795_LB1974_js006_N_A 100 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Sarcocystidae_Hammondia_hammondi_HHA1_v02 100 Alveolata_Chrompodelida_N_A_N_A_N_A_Vitrella_brassicaformis_merged_CCMP3155_Vbrassicaformis 100 100 100 Alveolata_Ciliophora_Spirotrichea_Sporadotrichida_Oxytrichidae_Oxytricha_trifallax_oxytricha_asm_v1.1 Alveolata_Ciliophora_Oligohymenophorea_Hymenostomatida_Tetrahymenidae_Tetrahymena_thermophila_N_A Alveolata_Colponemidia_N_A_N_A_N_A_N_A_N_A_merged_Colp15_Colp10 100 100 Stramenopila-Ochrophyta_N_A_Pelagophyceae_Pelagomonadales_N_A_Pelagomonas_calceolata_merged_RCC969_CCMP1756 100 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_rotula_CCMP3096 100 Stramenopila-Ochrophyta_N_A_Chrysophyceae_Chromulinales_Paraphysomonadaceae_Paraphysomonas_bandaiensis_js007 100 100 Stramenopila-Oomycota_N_A_Oomycetes_Saprolegniales_Saprolegniaceae_Saprolegnia_diclina_Sap_diclina_VS20_V1 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N_A_Thraustochytriaceae_Aplanochytrium_merged_kerguelense_sp 100 100 Rhizaria_N_A_N_A_N_A_N_A_N_A_N_A_D1 100 Rhizaria_Filosa_Chlorarachniophyceae_N_A_N_A_Bigelowiella_natans_N_A Rhizaria_Phytorhiza_N_A_N_A_Plasmodiophoridae_Plasmodiophora_brassicae_pbe3.h15 100 Telonemia_N_A_N_A_Telonemida_N_A_Telonema_subtile_merged_Tel-1_N_A 84 Telonemia_N_A_N_A_Telonemida_N_A_N_A_N_A_P-2 100 Haptista_Haptophyta_N_A_Prymnesiales_Prymnesiaceae_Prymnesium_parvum_merged_Texoma1_N_A 100 Haptista_Haptophyta_N_A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_merged_PLYM219_374_379_CCMP370_N_A 94100 Haptista_Haptophyta_N_A_Pavlovales_Pavlovaceae_merged_Pavlovales_N_A 100 Haptista_Centrohelida_N_A_N_A_Raphidiophryidae_Raphidiophrys_heterophryoidea_N_A Haptista_Centrohelida_N_A_N_A_Acanthocystidae_Choanocystis_sp_N_A 88 Haptista-sister_N_A_N_A_N_A_N_A_Ancoracysta_twista_TD Hemimastigophora_N_A_N_A_N_A_Spironemidae_Hemimastix_kukwesjijk_N_A 100 Opisthokonta-Fungi_Chytridiomycota_Chytridiomycetes_Spizellomycetales_Spizellomycetaceae_Spizellomyces_punctatus_S_punctatus_V1 100 Opisthokonta-Discicristoidea_N_A_N_A_N_A_Nucleariidae_Nuclearia_sp_SRR1617645 100 Opisthokonta-Filasterea_N_A_Ichthyosporea_N_A_N_A_Capsaspora_owczarzaki_merged_C_N_A 96 Opisthokonta-Metazoa_Chordata_Mammalia_Rodentia_Muridae_Mus_musculus_N_A 73 Apusomonadida_N_A_N_A_N_A_Apusomonadidae_Thecamonas_trahens_N_A 100 Breviatea_N_A_N_A_N_A_N_A_Pygsuia_biforma_N_A 89 Amoebozoa_Tubulinea_N_A_N_A_N_A_misidentifiedPessonella_sp_PRA-29 98 100 Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N_A_Dictyostelium_lacteum_ASM160615v1 Amoebozoa_Discosea_N_A_N_A_N_A_Stereomyxa_ramosa_Chinc5 100 Ancyromonadida_N_A_N_A_N_A_N_A_Nutomonas_longa_merged_SRR1617398_N_A 100 Ancyromonadida_N_A_N_A_N_A_Planomonadidae_Fabomonas_tropica_N_A 100 Excavata-Discoba_Percolozoa_Heterolobosea_N_A_N_A_Percolomonas_cosmopolitus_WS 100 Excavata-Discoba_Percolozoa_Heterolobosea_Schizopyrenida_Vahlkampfiidae_Naegleria_gruberi_N_A 75 Excavata-Discoba_Euglenozoa_N_A_Kinetoplastida_Bodonidae_Bodo_saltans_N_A 100 Excavata-Metamonada_Metamonada_N_A_Oxymonadida_Polymastigidae_Monocercomonoides_sp_PA203 Excavata-Metamonada_Metamonada_N_A_N_A_N_A_Paratrimastix_pyriformis_merged_js010_N_A

0.2

Supplementary Figure 15: Maximum likelihood tree of eukaryotic species showing the position of Picozoa. The tree is based on the concatenated alignment of 317 marker genes (filtered with Divvier) and was reconstructed using the PMSF approximation of the site-heterogeneous model LG+C60+F+G. Support values correspond to 100 non-parametric bootstrap replicates.

15 1 Archaeplastida-Rhodophyta_Rhodophyta_Compsopogonophyceae_Compsopogonales_Compsopogonaceae_Compsopogon_caeruleus_SAG36.94 1 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Porphyridium_purpureum_N/A 1 Archaeplastida-Rhodophyta_Rhodophyta_Stylonematophyceae_Stylonematales_Stylonemataceae_Rhodosorus_marinus_merged_UTEXLB2760_CCMP769 1 Archaeplastida-Rhodophyta_Rhodophyta_Bangiophyceae_Bangiales_Bangiaceae_merged_Porphyra_Pyropia 1 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gigartinales_Gigartinaceae_Chondrus_crispus_N/A

1 1 Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Cyanidioschyzon_merolae_N/A Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Galdieria_sulphuraria_N/A 1 Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_limneticus_N/A 1 Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_marinus_merged_Colp29_N/A 1 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A__merged_COSAG02_COSAG03_COSAG04_COSAG06 1 Picozoa_Picozoa_N/A_N/A_N/A_merged_Picobiliphyte_sp_MS584-11_COSAG05_COSAG01_SAG25 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_merged_SAG22_SAG31_SAG11 1 1 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Prasinococcales_N/A_Prasinoderma_singulare_RCC927 1 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Pyramimonadales_N/A_Pyramimonas_parkeae_CCMP726 1 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Volvocaceae_Volvox_carteri_N/A 1 Archaeplastida-Viridiplantae_Streptophyta_Bryopsida_Funariales_Funariaceae_Physcomitrella_patens_N/A 1 Archaeplastida-Viridiplantae_Streptophyta_N/A_Brassicales_Brassicaceae_Arabidopsis_thaliana_TAIR10 1 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_Gloeochaetales_Gloeochaetaceae_Gloeochaete_wittrockiana_SAG46.84 1 1 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_Cyanophoraceae_Cyanophora_paradoxa_N/A Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_N/A_Cyanoptyche_gloeocystis_SAG4.97 1 Cryptista_Cryptophyta_Cryptophyta_N/A_N/A_Cryptophyceae_sp_merged_CCMP2293_N/A 1 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Geminigera_merged_sp_cryophila 1 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Chroomonadaceae_Chroomonas_mesostigmatica_CCMP1168

1 1 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_merged_sp_avonlea Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_pacifica_merged_CCMP1869_N/A 1 Cryptista_Katablepharida_Katablepharidophyta_N/A_N/A_Roombia_truncata_N/A Cryptista_Palpitia_N/A_N/A_N/A__Palpitomonas_bilix_merged_NIES-2562_N/A 1 Alveolata_Dinophyta_Dinophyceae_Oxyrrhinales_Oxyrrhinaceae_Oxyrrhis_marina_merged_CCMP1795_LB1974_js006_N/A 1 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_merged_C15_C1 1 Alveolata_Chrompodelida_N/A_N/A_N/A_Vitrella_brassicaformis_merged_CCMP3155_Vbrassicaformis 1 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Sarcocystidae_Hammondia_hammondi_HHA1_v02 1 1 Alveolata_Ciliophora_Oligohymenophorea_Hymenostomatida_Tetrahymenidae_Tetrahymena_thermophila_N/A 1 Alveolata_Ciliophora_Spirotrichea_Sporadotrichida_Oxytrichidae_Oxytricha_trifallax_oxytricha_asm_v1.1 Alveolata_Colponemidia_N/A_N/A_N/A_N/A_N/A_merged_Colp15_Colp10 1 1 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_rotula_CCMP3096 1 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Pelagomonadales_N/A_Pelagomonas_calceolata_merged_RCC969_CCMP1756 1 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Paraphysomonadaceae_Paraphysomonas_bandaiensis_js007 1 1 Stramenopila-Oomycota_N/A_Oomycetes_Saprolegniales_Saprolegniaceae_Saprolegnia_diclina_Sap_diclina_VS20_V1 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Aplanochytrium_merged_kerguelense_sp 1 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Bigelowiella_natans_N/A 1 1 Rhizaria_N/A_N/A_N/A_N/A_N/A_N/A_D1 1 Rhizaria_Phytorhiza_N/A_N/A_Plasmodiophoridae_Plasmodiophora_brassicae_pbe3.h15 1 Telonemia_N/A_N/A_Telonemida_N/A_N/A_N/A_P-2 0.86 Telonemia_N/A_N/A_Telonemida_N/A_Telonema_subtile_merged_Tel-1_N/A 1 Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_merged_PLYM219_374_379_CCMP370_N/A 1 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Prymnesium_parvum_merged_Texoma1_N/A 1 1 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_merged_Pavlovales_N/A 1 Haptista_Centrohelida_N/A_N/A_Acanthocystidae_Choanocystis_sp_N/A Haptista_Centrohelida_N/A_N/A_Raphidiophryidae_Raphidiophrys_heterophryoidea_N/A Haptista-sister_N/A_N/A_N/A_N/A_Ancoracysta_twista_TD Hemimastigophora_N/A_N/A_N/A_Spironemidae_Hemimastix_kukwesjijk_N/A 1 Opisthokonta-Discicristoidea_N/A_N/A_N/A_Nucleariidae_Nuclearia_sp_SRR1617645 1 Opisthokonta-Fungi_Chytridiomycota_Chytridiomycetes_Spizellomycetales_Spizellomycetaceae_Spizellomyces_punctatus_S_punctatus_V1 1 1 Opisthokonta-Filasterea_N/A_Ichthyosporea_N/A_N/A_Capsaspora_owczarzaki_merged_C_N/A Opisthokonta-Metazoa_Chordata_Mammalia_Rodentia_Muridae_Mus_musculus_N/A 1 Apusomonadida_N/A_N/A_N/A_Apusomonadidae_Thecamonas_trahens_N/A

1 Breviatea_N/A_N/A_N/A_N/A_Pygsuia_biforma_N/A 0.97 Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N/A_Dictyostelium_lacteum_ASM160615v1 1 1 Amoebozoa_Tubulinea_N/A_N/A_N/A_misidentifiedPessonella_sp_PRA-29 Amoebozoa_Discosea_N/A_N/A_N/A_Stereomyxa_ramosa_Chinc5 1 1 Ancyromonadida_N/A_N/A_N/A_N/A_Nutomonas_longa_merged_SRR1617398_N/A Ancyromonadida_N/A_N/A_N/A_Planomonadidae_Fabomonas_tropica_N/A 1 Excavata-Metamonada_Metamonada_N/A_N/A_N/A_Paratrimastix_pyriformis_merged_js010_N/A 1 Excavata-Metamonada_Metamonada_N/A_Oxymonadida_Polymastigidae_Monocercomonoides_sp_PA203 1 Excavata-Discoba_Percolozoa_Heterolobosea_N/A_N/A_Percolomonas_cosmopolitus_WS 1 Excavata-Discoba_Percolozoa_Heterolobosea_Schizopyrenida_Vahlkampfiidae_Naegleria_gruberi_N/A Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Bodonidae_Bodo_saltans_N/A

0.3

Supplementary Figure 16: Bayesian phylogenetic tree made using PhyloBayes. The tree is based on the concatenated alignment of 317 marker genes (filtered with BMGE). Shown is the consensus of chains 1 and 2 (maxdiff 0.26) after 3600 cycles with 1500 cycles removed as burn-in. Support values correspond to posterior probability values.

16 1 Archaeplastida-Rhodophyta_Rhodophyta_Compsopogonophyceae_Compsopogonales_Compsopogonaceae_Compsopogon_caeruleus_SAG36.94 1 Archaeplastida-Rhodophyta_Rhodophyta_Porphyridiophyceae_Porphyridiales_Porphyridiaceae_Porphyridium_purpureum_N/A 1 Archaeplastida-Rhodophyta_Rhodophyta_Stylonematophyceae_Stylonematales_Stylonemataceae_Rhodosorus_marinus_merged_UTEXLB2760_CCMP769 1 Archaeplastida-Rhodophyta_Rhodophyta_Bangiophyceae_Bangiales_Bangiaceae_merged_Porphyra_Pyropia 1 Archaeplastida-Rhodophyta_Rhodophyta_Florideophyceae_Gigartinales_Gigartinaceae_Chondrus_crispus_N/A

1 1 Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Cyanidioschyzon_merolae_N/A Archaeplastida-Rhodophyta_Rhodophyta_Cyanidiophyceae_Cyanidiales_Cyanidiaceae_Galdieria_sulphuraria_N/A 1 Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_limneticus_N/A 1 Archaeplastida-Rhodelphea_N/A_N/A_Rhodelphida_Rhodelphidae_Rhodelphis_marinus_merged_Colp29_N/A 1 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A__merged_COSAG02_COSAG03_COSAG04_COSAG06 1 Picozoa_Picozoa_N/A_N/A_N/A_merged_Picobiliphyte_sp_MS584-11_COSAG05_COSAG01_SAG25 Picozoa_Picozoa_N/A_N/A_N/A_N/A_N/A_merged_SAG22_SAG31_SAG11 1 1 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Prasinococcales_N/A_Prasinoderma_singulare_RCC927 1 Archaeplastida-Viridiplantae_Chlorophyta_N/A_Pyramimonadales_N/A_Pyramimonas_parkeae_CCMP726 1 Archaeplastida-Viridiplantae_Chlorophyta_Chlorophyceae_Chlamydomonadales_Volvocaceae_Volvox_carteri_N/A 1 Archaeplastida-Viridiplantae_Streptophyta_Bryopsida_Funariales_Funariaceae_Physcomitrella_patens_N/A 1 Archaeplastida-Viridiplantae_Streptophyta_N/A_Brassicales_Brassicaceae_Arabidopsis_thaliana_TAIR10 1 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_Gloeochaetales_Gloeochaetaceae_Gloeochaete_wittrockiana_SAG46.84 1 1 Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_Cyanophoraceae_Cyanophora_paradoxa_N/A Archaeplastida-Glaucophyta_Glaucophyta_Glaucocystophyceae_N/A_N/A_Cyanoptyche_gloeocystis_SAG4.97 1 Cryptista_Cryptophyta_Cryptophyta_N/A_N/A_Cryptophyceae_sp_merged_CCMP2293_N/A 1 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Geminigeraceae_Geminigera_merged_sp_cryophila 1 Cryptista_Cryptophyta_Cryptophyta_Pyrenomonadales_Chroomonadaceae_Chroomonas_mesostigmatica_CCMP1168 1 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_merged_sp_avonlea 1 1 Cryptista_Cryptophyta_Cryptophyta_Cryptomonadales_Goniomonadaceae_Goniomonas_pacifica_merged_CCMP1869_N/A 1 Cryptista_Katablepharida_Katablepharidophyta_N/A_N/A_Roombia_truncata_N/A Cryptista_Palpitia_N/A_N/A_N/A__Palpitomonas_bilix_merged_NIES-2562_N/A 1 Haptista_Haptophyta_N/A_Isochrysidales_Noelaerhabdaceae_Emiliania_huxleyi_merged_PLYM219_374_379_CCMP370_N/A 1 Haptista_Haptophyta_N/A_Prymnesiales_Prymnesiaceae_Prymnesium_parvum_merged_Texoma1_N/A 1 Haptista_Haptophyta_N/A_Pavlovales_Pavlovaceae_merged_Pavlovales_N/A 1 Haptista_Centrohelida_N/A_N/A_Acanthocystidae_Choanocystis_sp_N/A Haptista_Centrohelida_N/A_N/A_Raphidiophryidae_Raphidiophrys_heterophryoidea_N/A 1 Alveolata_Dinophyta_Dinophyceae_Oxyrrhinales_Oxyrrhinaceae_Oxyrrhis_marina_merged_CCMP1795_LB1974_js006_N/A 1 Alveolata_Dinophyta_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_sp_merged_C15_C1 0.81 1 Alveolata_Chrompodelida_N/A_N/A_N/A_Vitrella_brassicaformis_merged_CCMP3155_Vbrassicaformis 1 Alveolata_Apicomplexa_Coccidia_Eucoccidiorida_Sarcocystidae_Hammondia_hammondi_HHA1_v02 1 1 Alveolata_Ciliophora_Oligohymenophorea_Hymenostomatida_Tetrahymenidae_Tetrahymena_thermophila_N/A Alveolata_Ciliophora_Spirotrichea_Sporadotrichida_Oxytrichidae_Oxytricha_trifallax_oxytricha_asm_v1.1 Alveolata_Colponemidia_N/A_N/A_N/A_N/A_N/A_merged_Colp15_Colp10 1 1 Stramenopila-Ochrophyta_Bacillariophyta_Coscinodiscophyceae_Thalassiosirales_Thalassiosiraceae_Thalassiosira_rotula_CCMP3096 1 Stramenopila-Ochrophyta_N/A_Pelagophyceae_Pelagomonadales_N/A_Pelagomonas_calceolata_merged_RCC969_CCMP1756 1 0.78 Stramenopila-Ochrophyta_N/A_Chrysophyceae_Chromulinales_Paraphysomonadaceae_Paraphysomonas_bandaiensis_js007 1 1 Stramenopila-Oomycota_N/A_Oomycetes_Saprolegniales_Saprolegniaceae_Saprolegnia_diclina_Sap_diclina_VS20_V1 Stramenopila-Sagenista_Labyrinthista_Labyrinthulomycetes_N/A_Thraustochytriaceae_Aplanochytrium_merged_kerguelense_sp 1 Rhizaria_Filosa_Chlorarachniophyceae_N/A_N/A_Bigelowiella_natans_N/A 1 1 Rhizaria_N/A_N/A_N/A_N/A_N/A_N/A_D1 1 Rhizaria_Phytorhiza_N/A_N/A_Plasmodiophoridae_Plasmodiophora_brassicae_pbe3.h15 1 Telonemia_N/A_N/A_Telonemida_N/A_N/A_N/A_P-2 Telonemia_N/A_N/A_Telonemida_N/A_Telonema_subtile_merged_Tel-1_N/A Haptista-sister_N/A_N/A_N/A_N/A_Ancoracysta_twista_TD Hemimastigophora_N/A_N/A_N/A_Spironemidae_Hemimastix_kukwesjijk_N/A 1 Opisthokonta-Discicristoidea_N/A_N/A_N/A_Nucleariidae_Nuclearia_sp_SRR1617645 1 Opisthokonta-Fungi_Chytridiomycota_Chytridiomycetes_Spizellomycetales_Spizellomycetaceae_Spizellomyces_punctatus_S_punctatus_V1

1 1 Opisthokonta-Filasterea_N/A_Ichthyosporea_N/A_N/A_Capsaspora_owczarzaki_merged_C_N/A Opisthokonta-Metazoa_Chordata_Mammalia_Rodentia_Muridae_Mus_musculus_N/A 1 Apusomonadida_N/A_N/A_N/A_Apusomonadidae_Thecamonas_trahens_N/A 1 Breviatea_N/A_N/A_N/A_N/A_Pygsuia_biforma_N/A 1 Amoebozoa_Evosea_Eumycetozoa_Dictyosteliida_N/A_Dictyostelium_lacteum_ASM160615v1 1 1 Amoebozoa_Tubulinea_N/A_N/A_N/A_misidentifiedPessonella_sp_PRA-29 Amoebozoa_Discosea_N/A_N/A_N/A_Stereomyxa_ramosa_Chinc5 0.98 1 Ancyromonadida_N/A_N/A_N/A_N/A_Nutomonas_longa_merged_SRR1617398_N/A Ancyromonadida_N/A_N/A_N/A_Planomonadidae_Fabomonas_tropica_N/A 1 Excavata-Metamonada_Metamonada_N/A_N/A_N/A_Paratrimastix_pyriformis_merged_js010_N/A 1 Excavata-Metamonada_Metamonada_N/A_Oxymonadida_Polymastigidae_Monocercomonoides_sp_PA203 1 Excavata-Discoba_Percolozoa_Heterolobosea_N/A_N/A_Percolomonas_cosmopolitus_WS 1 Excavata-Discoba_Percolozoa_Heterolobosea_Schizopyrenida_Vahlkampfiidae_Naegleria_gruberi_N/A Excavata-Discoba_Euglenozoa_N/A_Kinetoplastida_Bodonidae_Bodo_saltans_N/A

0.3

Supplementary Figure 17: Bayesian phylogenetic tree made using PhyloBayes. The tree is based on the concatenated alignment of 317 marker genes (filtered with BMGE). Shown is the consensus of chain 3 after 3600 cycles with 1500 cycles removed as burn-in. Support values correspond to posterior probability values.

17 Supplementary Table 1: Assembly/genome characteristics SAGs and CO-SAGs

Supplementary Table 2: Additional genomes added to the Phylogenomic dataset

Supplementary Table 3: Phylogenomic dataset taxon selection and taxon merging

Supplementary Table 4: Results from the AU and other topology tests performed with IQ-TREE

Supplementary Table 5: The Picozoan MS584-11 mitochondrial genome was used as a BLAST query into the 43 picozoan SAGs. Putative mitochondrial contigs were retrieved and used as queries into the NCBI nr database. If the top hit retrieved was MG202007.1, we considered the query sequence to be a bona fide mitochondrial contig.

Supplementary Table 6: Commonly retained plastid pathways and proteins

Supplementary Table 7: EGT clustering dataset taxon selection

Supplementary Table 8: Phylogenomic dataset taxon selection and taxon merging

Supplementary Table 9: EGT and LGT results for 33 selected species/groups

Supplementary Data 1: Untrimmed EEF2 alignment showing 2 amino acid signature in Rhodelphis, Rhodophyte, Chloroplastida, Cryptista, Haptophytes (but neither centrohelids not Ancoracysta) and Picozoa

18